dissenting.
With all due respect, I dissent from the majority’s view that the February 5, 2004 decision (“Decision”) of respondent State of Connecticut Department of Environmental Protection (“CTDEP”), denying the application of petitioner Islander East Pipeline Company (“Islander East”) for a Water Quality Certificate (“WQC”) under the Clean Water Act, 33 U.S.C. § 1251 et seq. (“CWA”), with respect to its proposed construction of a natural gas pipeline under Long Island Sound, was arbitrary and capricious. In my view, the Decision sufficiently indicates the basis for CTDEP’s order and reveals a rational connection between the facts found and the denial. We are not entitled to second-guess that decision merely because there is evidence in the record from which different inferences might have been drawn.
A. Jurisdiction
Preliminarily, I note my assumption that, under § 19 of the Natural Gas Act, 15 U.S.C. § 717r, as amended by the Energy Policy Act of 2005, Pub. L. No. 109-58, § 313(b), 119 Stat. 594, 689-90 (2005) (“EPACT”), this Court would have jurisdiction based on Ex parte Young, 209 U.S. 123, 28 S.Ct. 441, 52 L.Ed. 714 (1908), to entertain Islander East’s petition for review of the CTDEP Decision if we were to grant Islander East’s pending motion to add CTDEP’s Commissioner Gina McCarthy as a respondent. See, e.g., Verizon Maryland Inc. v. Public Service Commission, 535 U.S. 635, 645, 122 S.Ct. 1753, 152 L.Ed.2d 871 (2002) (a federal court may adjudicate a suit against a state official for prospective relief against an ongoing violation of federal law, even though the state itself, or its agency, would enjoy Eleventh Amendment immunity from the same suit). Islander East asks this Court to instruct CTDEP to “promptly issue a WQC to Islander East” (Islander East reply brief in support of petition at 23), which would permit Islander East to pursue its plan to construct the proposed pipeline. Plainly, the relief sought by Islander East is prospective. I would grant Islander East’s motion to add the Commissioner as a respondent, as I disagree with the majority’s view that that motion is moot.
I do not endorse the majority’s view that, in light of EPACT’s conferral of jurisdiction on the federal courts of appeals to review orders such as denials of CWA certificates, Connecticut has waived its sovereign immunity with respect to its denial of Islander East’s application for such a certificate. A state may of course waive its sovereign immunity; but for a waiver to be inferred from the state’s conduct, that conduct must have been “knowing[ ], cognizant of the [waiver] consequences.” Pennhurst State School & Hospital v. Halderman, 451 U.S. 1, 17, 101 S.Ct. 1531, 67 L.Ed.2d 694 (1981). CTDEP denied Islander East’s application in February 2004; EPACT was not enacted until August 2005. I cannot view CTDEP’s action in denying Islander East’s petition as a knowing waiver of sovereign immunity on the basis of a law that did not become effective until 18 months later.
The majority finds that Connecticut has waived its sovereign immunity in the present matter by failing to discontinue its participation in Clean Water Act regulation of natural gas pipeline projects after EPACT was enacted. I do not agree. The fact that Connecticut, with awareness of the effect of EPACT since mid-2005, elects to continue to decide applications for CWA certificates may perhaps constitute a waiver with respect to its post-EPACT decisions; but its present actions do not establish knowledge or voluntariness with respect to its past actions.
*107Finally, I disagree with the majority’s view that Connecticut lacks sovereign immunity on the theory that EPACT’s effect is merely procedural, see Majority Opinion ante at 93. Although jurisdictional statutes generally “speak to the power of the court rather than 'to the rights or obligations of the parties,” Landgraf v. USI Film Products, 511 U.S. 244, 274, 114 S.Ct. 1483 (1994) (internal quotation marks omitted), and although Landgraf does state that “[cjhanges in procedural rules may often be applied in suits arising before their enactment without raising concerns about retroactivity,” id. at 275, 114 S.Ct. 1483, I cannot regard an enactment that strips a state of immunity from suit as a matter of mere procedure. Sovereign immunity from suit is a privilege, see, e.g., College Savings Bank v. Florida Prepaid Postsecondary Education Expense Board, 527 U.S. 666, 681-82, 119 S.Ct. 2219, 144 L.Ed.2d 605 (1999); the elimination of that privilege is surely a matter of substance.
Nonetheless, the fact that CTDEP, a state agency, is immune from suit does not mean that relief under EPACT, if merited, would be unavailable. If Islander East’s motion to add the CTDEP Commissioner were granted, as discussed above there would be no sovereign-immunity bar to entertaining its petition, which seeks prospective relief; and “[wjhen the intervening statute authorizes or affects the propriety of prospective relief, application of the new provision is not retroactive,” Landgraf, 511 U.S. at 273, 114 S.Ct. 1488.
Accordingly, I turn to the merits of Islander East’s petition and the standard under which the petition is to be reviewed.
B. The Merits
1. Standard of Review
Although EPACT provides little guidance as to the contours of what it refers to as a “civil action for the review of an order,” 15 U.S.C. § 717r(d)(l), or as to the standard for review of such an order, I accept the proposition that, in this case, the proper standard is the arbitrary-and-capricious standard as set forth in the federal Administrative Procedure Act (“APA”), see 5 U.S.C. § 706. In conferring federal jurisdiction to review such decisions, EPACT groups orders of “a Federal agency” with orders of a “State administrative agency acting pursuant to Federal law,” 15 U.S.C. § 717r(d)(l); and where, as here, a state agency has acted as a “[CWA-]deputized regulator[ ] under the authority of federal law,” Majority Opinion ante at 90, I see no reason to apply to the state agency’s orders a review standard different from the APA arbitrary-and-capricious standard applicable to actions of federal agencies.
The APA provides, in pertinent part, that a court reviewing an agency decision is to set aside a decision that is “found to be ... arbitrary[ or] capricious,” and that in making such a determination, “the court shall review the whole record or those parts of it cited by a party.” 5 U.S.C. § 706 (emphasis added). Although the agency must provide some rational explanation for its decision, these APA provisions establish a standard of review that is deferential:
The scope of review under the “arbitrary and capricious” standard is narrow and a court is not to substitute its judgment for that of the agency. Nevertheless, the agency must examine the relevant data and articulate a satisfactory explanation for its action including a “rational connection between the facts found and the choice made.” Burlington Truck Lines, Inc. v. United States, 371 U.S. 156, 168, 83 S.Ct. 239, 9 L.Ed.2d 207 (1962). In reviewing that explanation, we must “consider whether the decision *108was based on a consideration of the relevant factors and whether there has been a clear error of judgment.” Bowman Transportation, Inc. v. Arkansas-Best Freight System, Inc., [419 U.S. 281, 285, 95 S.Ct. 438 (1974)]; Citizens to Preserve Overton Park v. Volpe, [401 U.S. 402, 416, 91 S.Ct. 814 (1971)]. Normally, an agency rule would be arbitrary and capricious if the agency has relied on factors which Congress has not intended it to consider, entirely failed to consider an important aspect of the problem, offered an explanation for its decision that runs counter to the evidence before the agency, or is so implausible that it could not be ascribed to a difference in view or the product of agency expertise. The reviewing court should not attempt itself to make up for such deficiencies; we may not supply a reasoned basis for the agency’s action that the agency itself has not given. SEC v. Chenery Corp., 332 U.S. 194, 196, 67 S.Ct. 1575, 91 L.Ed. 1995 (1947). We will, however, “uphold a decision of less than ideal clarity if the agency’s path may reasonably be discerned.” Bowman Transportation, Inc. v. Arkansas-Best Freight System, Inc., supra, at 286, 95 S.Ct. 438. See also Camp v. Pitts, 411 U.S. 138, 142-143, 93 S.Ct. 1241, 36 L.Ed.2d 106 (1973) (per curiam).
Motor Vehicle Manufacturers Ass’n of the United States, Inc. v. State Farm Mutual Automobile Insurance Co., 463 U.S. 29, 43, 103 S.Ct. 2856, 77 L.Ed.2d 443 (1983) (“State Farm”) (emphases added); see also id. at 42, 103 S.Ct. 2856 (“[U]nder this standard, a reviewing court may not set aside an agency rule that is rational, based on consideration of the relevant factors[,] and within the scope of the authority delegated to the agency by the statute.”).
“A court reviewing an agency’s adjudicative action should accept the agency’s factual findings if those findings are supported by substantial evidence in the record as a whole.” Arkansas v. Oklahoma, 503 U.S. 91, 113, 112 S.Ct. 1046, 117 L.Ed.2d 239 (1992) (emphasis omitted); see also State Farm, 463 U.S. at 44, 103 S.Ct. 2856 (agency’s factual findings are to be upheld if “supported by substantial evidence on the record considered as a whole” (emphasis added) (internal quotation marks omitted)). Since an agency’s findings are to be upheld if they are supported “by substantial evidence on the record as a whole,” State Farm, 463 U.S. at 44, 103 S.Ct. 2856 (emphasis added), the statement in State Farm that an order may be found arbitrary and capricious if it “runs counter to the evidence before the agency,” id. at 43, 103 S.Ct. 2856 (emphasis added), means that it may be so found if it runs counter to all of the substantial evidence. Thus, the Court has stated that this facet of the arbitrary-and-capricious determination is in essence a “deci[sion as to] whether on th[e] record it would have been possible for a reasonable jury to reach the [agency’s] conclusion,” Allentown Mack Sales & Service, Inc. v. NLRB, 522 U.S. 359, 366-67, 118 S.Ct. 818, 139 L.Ed.2d 797 (1998) (emphasis added). Where there is evidence in the record from which a reasonable jury could have reached the agency’s decision, the “court is not to substitute its judgment for that of the agency,” State Farm, 463 U.S. at 43, 103 S.Ct. 2856.
The majority takes the position that “[i]t is not our province to mine the record for evidence that would support [an agency decision].” Majority Opinion ante at 100. That characterization of the scope of review confuses the reasons for a decision with the evidence to support that decision. We are not to supply the rationale for an agency decision; but where the agency has stated its rationale, or where its rationale “may reasonably be discerned,” State *109Farm, 463 U.S. at 43, 103 S.Ct. 2856, we are required to “review the whole record,” 5 U.S.C. § 706, and to uphold the agency decision if it is “supported by substantial evidence on the record considered as a whole,” State Farm, 463 U.S. at 44, 103 S.Ct. 2856 (internal quotation marks omitted).
Given these principles, I cannot conclude that CTDEP’s denial of Islander East’s application should be disturbed.
2. The Contents of the CTDEP Decision
Preliminarily, I note that the CTDEP Decision is not so sketchy as the majority suggests. Although the text of the Decision is six pages, the Decision annexes and refers to appendices covering some 300 pages. The appendices to the Decision include a United States Environmental Protection Agency-funded survey of water quality in Long Island Sound (see Decision Appendix B); a report on “Potential Sedimentation Impacts Which Could Result from Dredging,” authored by Roberge Associates Coastal Engineers, LLC, comprising a series of analyses, dated May 5, 2003, September 30, 2003, and February 4, 2004 (collectively the “Roberge Reports”), of the likely effects of the Islander East pipeline as initially proposed and as subsequently amended (see Decision Appendix E); a report by coastal resource analyst Peter H. Pellegrino entitled “Macrobenthic Community Structure along the Proposed Islander East Gas Pipeline Route in Long Island Sound” (“Pellegrino Report”) (see Decision Appendix F); and a 12-page July 29, 2003 letter from CTDEP to Islander East explaining CTDEP’s objections to Islander East’s initial proposal and requesting additional specified information (see Decision Appendix G). Materials that an agency cites and attaches to its decision must be taken into account in determining whether the decision is arbitrary and capricious. See 5 U.S.C. § 706.
Given the text of the CTDEP Decision, which I attach as an appendix to this dissent, and the contents of the Appendices that were appended to the Decision, I think it clear that CTDEP denied Islander East’s application on the basis that the proposed pipeline, which is not a water-dependent use, would be routed through prime shellfish habitat, would have a lengthy, significant, adverse impact of unknown duration on the shellfish industry, and would displace the obviously water-dependent activity of shellfishing. (See Decision at 2-6.)
The majority appears to suggest that the shellfish-injury rationale is a creation of this dissent rather than a rationale given by CTDEP, as the majority opinion (a) states that “[t]he dissent points to portions of the record indicating that installation would directly harm large areas of the substrate, disturb shellfish habitats, and cause significant shellfish mortality in certain locations,” and (b) continues by stating, “[hjowever, ‘we may not supply a reasoned basis for the agency’s action that the agency itself has not given,’ ” Majority Opinion ante at 99-100 (quoting State Farm, 463 U.S. at 43, 103 S.Ct. 2856). In suggesting that injury to shellfish and the shellfish industry was not a basis relied on by CTDEP (and in stating as well that CTDEP “fail[ed] to identify with any specificity the shellfish communities that would be impacted by the pipeline,” Majority Opinion ante at 101), the majority ignores even the text of the Decision. With respect to the issue of shellfish habitat alteration, the Decision stated in part as follows:
Islander East has proposed a regulated activity in coastal waters of the State in the nearshore waters of the Thimble Islands complex in the Town of Bran-*110ford. Overall, chemical and bacteriological water quality conditions in this location are consistently excellent....
In concert with excellent water quality, the Thimble Islands region also exhibits an abundance of high quality habitat. These physical conditions combine to support a diverse and abundant assemblage of marine life.... The United States Fish and Wildlife Service, for example, has designated this particular area a “significant habitat complex in need of protection.” In addition to providing habitat for a variety of de-mersal and pelagic species, these diverse bottom habitats of the Thimble Islands region also support eastern oyster CCrassostrea virginica), hard clams (.Mercenaria mercenaria), soft clams (.Mya arenaria), blue mussels (Mytilus edulis), and channel whelk (Busycon canaliculatum).
These species, clams and oysters in particular, support significant commercial shellfish harvesting operations. The pipeline corridor, as proposed by Islander East, is sited within and adjacent to extensive shellfish grants, leased shellfish grounds and public shellfishing lands. The submerged land through which the pipeline route is proposed that is not currently leased is also productive shellfish habitat and is significant for potential future expansion of the shellfish industry, particularly in as much as the western reaches of Long Island Sound have been more affected in recent decades by lower dissolved oxygen levels and other environmental impacts that affect shellfish and benthic abundance. The shellfish industry is an economically-significant and long-established water-dependent use in Connecticut. In fact, Connecticut’s nationally-recognized shellfish industry produces the highest quality oysters in the United States.... The shellfishing industry in the Thimble Islands region thrives because of the excellent water quality and exceptional habitat conditions. ...
[T]he water is of sufficiently high quality to allow for direct consumption of shellfish from these beds without the requirement for relocation and depuration of the shellfish prior to human consumption .... [T]he waters off Branford support approximately 46% of shellfishing areas approved for direct harvest in eastern Connecticut....
.... Th[e] proposed installation would include dredging, plowing, backfilling, equipment anchoring, and anchor cable sweeping. These activities would result in negative impacts to both the water quality and substrate. Turbidity of the water column would be relatively short-term. When this material precipitates out of the water column, it will result in sediment deposition on the benthic substrate. At the request of the Town of Branford’s Blue Ribbon Committee, John Roberge, P.E., LLC, prepared an assessment of sedimentation impacts associated with pipeline installation as modified by Islander East to mitigate sediment dispersion. The following sediment deposition pattern was estimated in Mr. Roberge’s study:
1 mm up to 100 meters from the trench centerline (approximately 70 acres); and
3 mm up to 40 meters from the trench centerline (approximately 35 acres).
The Department has determined that the negative impacts resulting from this depositional layer, in addition to direct substrate disturbance associated with dredging, plowing, backfilling, equipment anchoring, and anchor cable sweeping, are inconsistent with the *111Water Quality Standards. Pipeline installation would not only temporarily disturb water quality, it would permanently change the substrate and negatively impact the existing aquatic biota that depend on such substrate. The Connecticut Water Quality Standards define biological integrity as the ability of any aquatic ecosystem to support and maintain a balanced, integrated, adaptive community of organisms having a species composition, diversity, and functional organization comparable to that of the natural habitats of a region. The combined assaults of direct habitat disturbance and temporary water quality impacts resulting in sediment deposition negatively impact the overall biological integrity of the Thimbles [sic] Islands ecosystem and are therefore inconsistent with Standard No. 1 of the Connecticut Water Quality Standards.
Pipeline installation through the Thimble Islands ecosystem will dramatically alter natural habitats and adversely impact the existing community of organisms. As discussed in a study entitled “Macrobenthie Community Structure Along The Proposed Islander East Pipeline Route In Long Island Sound,” by Pellegrino, there are dramatic differences in community structure associated with a disturbed versus a non-disturbed substrate. Once the original bottom has been disturbed, a soft sediment, referred to as the nephloide layer, covers the bottom and fills in any depressions left on the disturbed surface. Thus, the high-order or late successional stage species such as clams and oysters that lived in the original substrate can no longer exist. The community structure of the original substrate changes to that of early-stage opportunistic species such as polychaete worms. It is uncertain whether the associated diverse assemblage of bottom dwelling organisms currently present in this area could be reestablished. No studies exist from which one may predict a known recovery time for both these benthic communities and the substrate, if, indeed, there is any significant recovery.
(Decision at 2-4 (footnotes omitted) (emphases added).) Thus, it is clear that CTDEP denied Islander East’s application based principally on the finding, in short, that if its project were carried out, where now there is an abundance of oysters and clams, there could well be only worms.
CTDEP also noted that the Connecticut antidegradation policy requires the maintenance and protection of water quality in high-quality-water areas and “mandates that existing uses must continue to be supported in all cases.” (Decision at 4.) The Decision stated that the above findings showed that the Islander East pipeline would not be consistent with this policy:
As previously described, the pipeline is proposed to be sited within and adjacent to extensive shellfish grants, leased shellfish grounds and public shellfish lands. The discharge of backfill associated with pipeline installation would result in approximately 5.5 acres of near-shore bottom habitat being permanently degraded and rendered unsuitable for supporting the diverse assemblage of shellfish and other bottom dwelling organisms currently inhabiting this area.
(Id.) The Decision concluded that CTDEP had
determined that the regulated activity in the proposed location will permanently alter the existing high quality physical and biological integrity and productivity of this area to the extent that the existing uses for habitat for marine fish, other aquatic life and wildlife and shellfish *112harvesting for direct human consumption will be impaired. Essential shellfish habitat will be lost due to the temporary and permanent alteration of the benthic environment resulting from the proposed work. Finally, the siting of the non-water dependent pipeline through prime shellfish habitat would cause a significant and permanent adverse impact to a water-dependent use by displacing the water-dependent use of shellfishing with the non-water-dependent use of natural gas transmission.
(Id. at 6 (emphases added).)
The majority states that CTDEP failed to cite any studies or record evidence to support its findings. See, e.g., Majority Opinion ante at 97 (“The CTDEP cited no scientific studies or other evidence that directly supported the ... findings” that the “sediment deposition and direct benthic substrate disturbances resulting from installation would ‘permanently change the substrate and negatively impact the existing aquatic biota that depend on such substrate.’ ” (quoting Decision at 4)). The majority also states that CTDEP
failed to mention that at least four scientific studies in the record concluded that the substrate was capable of a return to its existing condition — -findings directly opposite to its conclusion that pipeline installation would “permanently change the substrate” and “dramatically alter natural habitats.”
Majority Opinion ante at 97 (quoting Decision at 4). By these “opposite” opinions, the majority apparently refers to (1) an opinion by consulting marine biologist Dr. Roman Zajac (“Zajac opinion”); (2) a report by TRC Environmental Corp. entitled “Evaluation of Benthic Impacts Associated with Islander East’s Modified Offshore Construction Techniques” (“TRC Report”), which quotes and relies on the Zajac opinion; (3) a report by the Garrett Group, Ltd., entitled “Preliminary Report on the Anticipated Biological Impacts Associated with the Proposed Islander East Pipeline Project, Through the Nearshore Area of Long Island Sound — Branford, Connecticut” (“Garrett Group Report”); and (4) the Pellegrino Report. See Majority Opinion ante at 97-98.
But both the contention that CTDEP cited nothing to support its findings and the contention that CTDEP failed to consider the “opposite” opinions are contradicted by the record. First, CTDEP pointed out that coastal engineering consultant John Roberge had “prepared an assessment of sedimentation impacts associated with pipeline installation as modified by Islander East to mitigate sediment dispersion” (Decision at 3), and it attached his series of reports to the Decision as Appendix E (see id. n. 10). The Roberge Reports predicted that “benthic species will likely be killed even in areas receiving a thin veneer of deposited sediments” (Ro-berge Report dated February 4, 2004, at 2; Roberge Report dated September 30, 2003, at 3) and that “[tjhis seafloor burial has the potential to result in significant mortality within the benthic communities” (Roberge Report dated February 4, 2004, at 3; Roberge Report dated September 30, 2003, at 4). In making this prediction, the Roberge Reports stated, inter alia, that the Islander East pipeline would cover 69.8 acres with up to 1 mm of sediment and cover 34.9 acres with up to 3 mm of sediment, and noted that a study by the United States Army Corps of Engineers had found “that sediment deposits of up to 1 mm will cause up to 50% mortality, and deposits of up to 2 mm will cause 100% mortality to some benthic species.” (Ro-berge Report dated February 4, 2004, at 3 (emphasis added); Roberge Report dated September 30, 2003, at 4 (emphasis add*113ed)). This evidence supported CTDEP’s finding that the Islander East pipeline would have an adverse and permanent effect on the makeup of the benthic community.
Second, the Roberge Reports expressly mentioned two of the studies on which the majority relies for the opposite conclusion: As reported in the “Preliminary Report
on the Anticipated Biological Impacts Associated with the Proposed Islander East Pipeline Project, through the Nearshore Area of Long Island Sound-Branford, CT”, prepared, by The Garrett Group, LTD and dated May 8, 2003, near and far-field deposition of suspended solids may cause a measurable cover, or a thin veneer of fíne particles cover over proximal hard bottom substrate. The Garrett report references benthic studies performed by the US Army Corps of Engineers (LaSalle et all [sic] 1991) which note[ ], contrary to Dr. Za-jac’s opinion, that sediment deposits of up to 1 mm will cause up to 50% mortality, and deposits of up to 2 mm will cause 100% mortality to some benthic species.
(Decision Appendix E, Roberge Report dated February 4, 2004, at 2 (emphases added); Roberge Report dated September 30, 2003, at 4 (emphases added).) Although the majority opinion states that “any conclusions that Roberge ... made as to mortality caused by sedimentation apparently were drawn from, the Garrett Report, which found that sedimentation would not cause permanent damage,” Majority Opinion ante at 98-99 (emphasis added), it is plain from the above language of the Roberge Reports themselves that the Roberge Reports explicitly rejected the views of the Garrett Group and Dr. Zajac in light of the contrary findings of the Army Corps of Engineers — in studies to which the Garrett Group Report itself had adverted. Further, given the reliance of the TRC Report on the opinion of Dr. Zajac, see Majority Opinion ante at 97 (quoting TRC Report’s quotation of the Zajac opinion), the Roberge Reports can properly be regarded as implicitly rejecting the views of the TRC Report as well. Although the majority suggests that CTDEP should have granted Islander East’s application based on the reports such as that of the Garrett Group, it is the very antithesis of “deferential” review to conclude that an agency was required to credit a report that cites evidence contradicting the report’s own conclusions.
The fourth report advanced by the majority as one of the “opposite” opinions supposedly ignored by CTDEP is the Pel-legrino Report. The majority’s suggestion that this report was ignored by CTDEP is peculiar, given that the report is annexed to the Decision as Appendix F. Further, the majority’s reliance on the Pellegrino Report as a basis for the conclusion that the CTDEP Decision is arbitrary and capricious is puzzling. The conclusion of this report stated that “[t]he structure of benthic communities is usually controlled by infrequent severe events (disturbances) that disrupt the community and return the successional process to an earlier stage,” and that the “recovery process in soft-sediment communities is characterized by a succession of community types, usually beginning with the appearance of opportunistic species,” ie., polychaete worms, and eventually “progressing to the establishment of high order ... successional assemblages,” such as bivalves and gastropods (Pellegrino Report at 6 (emphasis added)); but the Pellegrino Report contained no discussion whatsoever of the impact on such communities by a pipeline construction process — a process that surely is not the “usual[]” type of “disturbance! ].” Indeed, the stated purpose of the Pellegrino Report was simply to describe the results of a benthic survey along *114the proposed Islander East pipeline route, in order “to document existing benthic community structure and to provide a benthic baseline against which future changes may be detected.” (Id. at 2.)
In sum, I cannot agree with the majority’s view that the CTDEP “fail[ed] to acknowledge the existence of the above studies,” Majority Opinion ante at 98 n. 13. I think it appropriate, in conducting a review that is to be deferential, to infer that CTDEP must have acknowledged the study it attached to its Decision and, in relying on the Roberge Reports, implicitly acknowledged the existence of studies that were explicitly mentioned and disputed in the Roberge Reports.
I note that the majority also relies on many statements in the Final Environmental Impact Statement (“FEIS”) on Islander East’s proposed pipeline, issued by the United States Federal Energy Regulatory Commission (“FERC”), see, e.g., Majority Opinion ante at 96-97, 99. The FEIS, however, also included many findings not mentioned by the majority that are consistent with CTDEP’s conclusion that the Islander East pipeline would adversely impact benthic communities. For example, the FEIS indicates that construction of the trench and installation of the pipeline would directly impact 3,140 acres of Sound bottom, including 298 acres disturbed by trenching, 23.8 acres by the creation of an “exit hole” needed for horizontal directional drilling, 2,807 acres disturbed by cable sweep, and 9.7 acres by anchor strikes. (See FEIS at 3-45.) Islander East expected to make more than 2,000 anchor strikes, each causing a 1376-cubic-foot hole in the Sound floor (see id. at 3-65); “lobsters ... in the direct area of anchor placement would suffer mortality” (id. at 3-72), and “[t]he persistence of these depressions would represent a long-term conversion of benthic habitat” (id. at 3-65 (emphasis added)); “[d]ue to the weight of the anchor and the depth of the [anchor] scar, the impact on shellfish likely would be complete mortality within the footprint of the scar” (id. at 3-71 (emphasis added)). The record shows that CTDEP had considered the FEIS. (See Decision Appendix G at 9 (“Staff have reviewed FERC’s Final Environmental Impact Statement (FEIS) FERC/EIS-0143F dated August 2002.”).)
The majority repeatedly faults the CTDEP Decision for “not point[ing] to evidence” in support of its rationale that the shellfish industry would be negatively impacted, Majority Opinion ante at 101 (emphasis added); see also id. (Decision “fails to point to even one specific lease that would be impacted”), and states that “ ‘[t]he reviewing court should not attempt itself to make up for such deficiencies,’ ” id. at 101-02 (quoting State Farm, 463 U.S. at 43, 103 S.Ct. 2856). However, as can be seen from the more complete State Farm passage quoted above in Part B.l. of this dissent, the Supreme Court’s reference to “such” deficiencies did not include a failure to “point to evidence,” Majority Opinion ante at 104; rather, that passage referred to an agency’s reliance on factors unintended by Congress, or an “entire[]” failure “to consider an important aspect of the problem,” or proffering of explanations “so implausible that [they] could not be ascribed to a difference in view or the product of agency expertise,” State Farm, 463 U.S. at 43, 103 S.Ct. 2856.
Further, I disagree with the majority’s view that the record evidence indicates with certainty “that direct pipeline installation and accompanying sediment deposition would not have a permanent effect on the benthic environment,” Majority Opinion ante at 97 (emphasis added). The majority cites the FEIS and the four “opposite” opinions that it contends CTDEP *115failed to consider. But not only does the record indicate, as discussed above, that these sources were considered by CTDEP; the record also reveals that the reports themselves do not match the majority’s certainty. For example, the TRC Report states that the anticipated “degree of sediment deposition ... should have little impact on sea floor habitats and communities, and may approach background/natural levels of sediment resus-pension and deposition in the area,” but only “if the predictions are correct.” (TRC Report at 5 (emphases added) (internal quotation marks omitted).) The FEIS states that “recovery of most of the disturbed benthic communities along the pipeline route could be expected to occur within 2 to 5 years” (FEIS at 3-66 (emphasis added)) but that “some portions of shellfish habitat may remain unproductive for many years due to trenching activities” (id. at 3-70 (emphasis added)). And while the Garrett Group Report states at one point that “the bottom mil recover after several years” (Garrett Group Report at ES-2 (emphasis added)), this is said to be based on the Garrett Group’s “professional experience ... that bottom recoveries typically require several years in the absence of additional activity” (id. at 5 (emphasis added)), and that report itself acknowledges that “[rjecolonization of bottom disturbances can vary dramatically” (id. at ES-1 (emphasis added)).
It was hardly irrational, therefore, for CTDEP to conclude from these hedged opinions that “[n]o studies exist from which one may predict a known recovery time.” (Decision at 4 (emphasis added).) Not one of the reports relied on by the majority was unequivocal; and CTDEP’s own experience with the Iroquois Pipeline project' — completed more than a dozen years earlier — supported CTDEP’s view that the adverse impacts of such a project were likely permanent. CTDEP stated that habitat lost in the Iroquois Pipeline installation in 1991 “has not recovered to date.” (Decision Appendix G at 6 (emphasis added).)
Although the majority states that the Iroquois Pipeline installation is not comparable because Islander East proposes to use horizontal directional drilling (“HDD”), rather than dredging, in order to mitigate topography problems, the record does not indicate that Islander East carried its burden of showing that that proposal would have a substantial mitigating effect. The total length of the proposed pipeline was to be 44.8 miles, of which 22.7 miles would be under the waters of Long Island Sound. While the majority opinion might give the impression that nearly half of the pipeline to be laid underwater would be installed by means of HDD, see Majority Opinion ante at 87 (describing the proposed HDD as “initiaflmg] the pipeline installation at a point onshore in Connecticut, approximately 700 feet inland from the shoreline [and] continuing] until mile post (MP) 10.9”), in fact mile post 10.9 is only 3,500 feet offshore. The mile posts begin in North Haven, Connecticut, 10.1 miles from the point in Branford at which the pipeline was to enter the Sound. (See FEIS at 2-12.) Thus, Islander East planned to use HDD under water only for the nearshore 3,500 feet of the pipeline (see Decision at 3), i.e., less than two-thirds of one mile, and not for the remaining 22+ miles of underwater installation. For the 97% of the underwater section of the pipeline in the Thimble Islands region and beyond, Islander East proposed to dredge and plow, as was done for the Iroquois Pipeline. And the needed HDD exit hole — -a 23.8-acre underwater pit that would be the dirtiest part of the pipeline installation, as it must be created by mechanical dredging and is the area into which the muds and lubricants used in the HDD process would *116be spewed (see FEIS at 3-49, 3-52 to 3-53) — would have been less than one-tenth of a mile from the Thimble Islands and their (currently) especially-clean waters (see Decision Appendix C).
Finally, the majority states that CTDEP “fails to support” its “claim that an area of 3,700 acres would be impacted” by the Islander East pipeline, Majority Opinion ante at 100-01, and states that “[t]he FEIS refers to a total impacted area of only 3,140 acres,” Majority Opinion ante at 101. It does not appear to me that the CTDEP Decision was intended to mean that all 3,700 acres would be uniformly impacted. The Decision states that “topographic irregularities” would occur “over the entire 3,700-acre Islander East corridor,” Decision at 5 (emphasis added), and it is plain that the pipeline construction process would not result in uniform conditions on the floor of the Sound. The FEIS, for example, discussed the fact that Islander East proposed to make 2,628 anchor strikes (see FEIS at 3-65); each of them would cause a 1376-cubic-foot hole in the Sound floor (see id. at 3^45, 3-65), holes that would “persist[ ]” and cause “a long-term conversion of benthic habitat” (id. at 3-65). In any event, even if “only 3,140,” Majority Opinion ante at 101 (emphasis added), out of 3,700 acres would be impacted as the FEIS found, I would be hard-pressed to find that an absence of anticipated impact on 560 acres out of 3,700 (i.e., 15% of the project) made the denial of the requested permit arbitrary and capricious.
To summarize, the CTDEP Decision explained that the Islander East application was being denied because construction of the pipeline planned by Islander East — to be routed through the waters of the Thimble Islands, a thriving shellfishing area that the United States Fish and Wildlife Service has designated as a significant habitat complex in need of protection— would likely permanently change the benthic substrate, depositing layers of sediment in which clams and oysters, which lived in the original substrate, could no longer survive; that this would have adverse effects on shellfish and the shellfish industry, given that although early-stage opportunistic species such as polychaete worms could be expected to return to the areas disturbed by pipeline construction, it is uncertain when the higher-order organisms currently present in these areas would return, if ever. CTDEP’s denial and rationale are supported by evidence in the record as a whole, and other opinions were addressed in reports cited by CTDEP and attached to its Decision. Accordingly, I dissent from the majority’s conclusion that CTDEP’s Decision is arbitrary and capricious.
APPENDIX A
CTDEP DECISION of February 5, 2004, DENYING WATER QUALITY CERTIFICATE
[omitting only a paragraph that addressed the Connecticut Coastal Management Act, on which CTDEP places no reliance]
On March 14, 2003, the Islander East Pipeline Company, LLC (“Islander East”) submitted a Water Quality Certificate (WQC) application for discharges to the waters of the State pursuant to Section 401(a)(1) of the Federal Clean Water Act (the “Act”), as amended. The proposed activity includes the upgrade of an existing natural gas transmission pipeline system in Cheshire and North Haven and installation of a new 24" diameter pipeline in East Haven, North Branford and Branford continuing across Long Island Sound to Brookhaven, New York.
Determination
The proposed work was evaluated for compliance with the applicable provisions *117of sections 301, 302, 303, 306 and 307 of the Act, the State of Connecticut’s Water Quality Standards including the Connecticut Anti-Degradation Implementation Policy, and Water Quality Criteria adopted pursuant to Section 22a-426 of the Connecticut General Statutes and the goals and policies of Chapter 444 of the Connecticut General Statutes. Based on this review, the Department of Environmental Protection (“Department”) has determined that the proposed work in the proposed location is inconsistent with the Water Quality Standards. The work, as proposed, would adversely affect water quality and prohibit the existing and designated uses of the receiving waters. Accordingly, the Department hereby denies Water Quality Certification of Application # 200300937 in accordance with Section 401(a)(1) of the Clean Water Act.
Connecticut Water Quality Standards
Section 303 of the Act requires that states adopt surface water quality standards. These state water quality standards are submitted to, and must be approved by, the Administrator of the U.S. Environmental Protection Agency (“EPA”). State water quality standards provide the basis for water quality management decision-making by the Department and are a critical component in the state’s efforts to achieve the fundamental goal established in the Act of protecting and maintaining the physical, chemical, and biological integrity of the nation’s waters. At a minimum, the standards must be sufficient also to meet the interim goals of the Act for achieving water quality conditions that allow for protection and propagation of fish, shellfish, and wildlife, and for recreation in and on the water.
As required by the Act, Connecticut’s Water Quality Standards include:
• beneficial designated uses for each wa-terbody (e.g., aquatic life, swimming, drinking, navigation, etc.) that are assigned on the basis of the waterbody’s classification;
• narrative and/or numeric water quality criteria that must be met to support each designated use; and
• policy statements including an anti-degradation policy and implementation procedures designed to maintain and protect water quality in high quality waters, and protect and maintain existing uses in all cases.22
These elements do not stand alone, but must be read in such a fashion as to be internally consistent within the Water Quality Standards and consistent with the goals of the Act.
Coastal Water Classification and Designated Uses
Islander East has proposed a regulated activity in coastal waters of the State in the nearshore waters of the Thimble Islands complex in the Town of Branford. Overall, chemical and bacteriological water quality conditions in this location are consistently excellent. Long-term water quality monitoring initiated in 1991 by the Department as part of the Long Island Sound Study23 shows that only rarely are these waters subjected to the impacts of low dissolved oxygen conditions that gen*118erally develop each summer in areas farther to the west in Long Island Sound.24 The resulting water quality classifications for this region are SB/SA and SA.25 The SB/SA Classification signifies that the water quality management goal is to achieve full support of all Class SA designated uses. Class SA waters are designated for habitat for marine fish, other aquatic life and wildlife; shellfish harvesting for direct human consumption; recreation; industrial water supply; and navigation.26
In concert with excellent water quality, the Thimble Islands region also exhibits an abundance of high quality habitat. These physical conditions combine to support a diverse and abundant assemblage of marine life. The Thimble Islands typically emerge from relatively shallow waters, approximately 30' deep. In addition to this significant area of shallow water-land interface where biological diversity is rich and productive, this area hosts unique sub-tidal conditions including submerged rock reefs and a diversity of benthic habitats that range from soft mud to compacted sand and gravel all of which contribute to the biological integrity of the aquatic ecosystem. The United States Fish and Wildlife Service, for example, has designated this particular area a “significant habitat complex in need of protection.” 27 In addition to providing habitat for a variety of demersal and pelagic species, these diverse bottom habitats of the Thimble Islands region also support eastern oyster CCrassostrea virginica), hard clams (Mercenaria mercenaria), soft clams (Mya arenaria), blue mussels (Mytilus edulis), and channel whelk (Busycon canalicula-tum).
These species, clams and oysters in particular, support significant commercial shellfish harvesting operations. The pipeline corridor, as proposed by Islander East, is sited within and adjacent to extensive shellfish grants, leased shellfish grounds and public shellfishing lands. The submerged land through which the pipeline route is proposed that is not currently leased is also productive shellfish habitat and is significant for potential future expansion of the shellfish industry, particularly in as much as the western reaches of Long Island Sound have been more affected in recent decades by lower dissolved oxygen levels and other environmental impacts that affect shellfish and benthic abundance. The shellfish industry is an eeonomically-signifieant and long-established water-dependent use in Connecticut. In fact, Connecticut’s nationally-recognized shellfish industry produces the highest quality oysters in the United States. Despite a devastating blow to oyster production from MSX28 in 1997, the annual com*119mercial landing statistics, provided by the National Oceanic and Atmospheric Administration-Fisheries, Connecticut continues to compete nationally and in 2001 was ranked first in hard clam production on the east coast and second for oyster market harvest.
The shellfishing industry in the Thimble Islands region thrives because of the excellent water quality and exceptional habitat conditions. Of particular importance to maintaining the existing shellfishing use of this area is authorization by the State of Connecticut Department of Agriculture, Aquaculture Division (DA/AD) for harvest of shellfish for direct human consumption. The DA/AD “Approved” designation, which is the most stringent and, therefore, the most difficult to achieve, recognizes that the water is of sufficiently high quality to allow for direct consumption of shellfish from these beds without the requirement for relocation and depuration of the shellfish prior to human consumption (see map in Appendix D). Although many of Connecticut’s marine waters are classified SA or SB/SA, the designated areas where suitable habitat exists and monitoring data documents the exceptionally good water quality necessary to receive an “Approved” designation by DA/AD are in fact limited. In general, the waters off Branford support approximately 46% of shellfishing areas approved for direct harvest in eastern Connecticut.29 A more detailed description of the specific parameters and required criteria relating to authorization for direct harvest of shellfish is referenced in the Water Quality Standards at page seventeen (Appendix A).
Water Quality Impacts and Habitat Alteration
The landward-most segment of pipeline, approximately 3500 feet, is proposed to be installed in-water from Juniper Point utilizing the horizontal directional drilling (HDD) method. At the HDD exit point a pit of approximate dimensions 18' deep x 130' wide x 310' long is proposed to be excavated. From this exit pit, a trench approximately 5' deep x 37' wide x 5520' long is proposed to be dredged to approximately Milepost 12. (A trench width of 37' is based on a 3:1 angle of repose.) The exit pit and 5520' long trench are proposed to be backfilled with bank-run gravel. From Milepost 12 for nine miles to the Connecticut/New York state line, three passes of a sub-sea plow are proposed to: create a trench 5' deep x 25' wide at the top of slope; lay the pipe; and backfill previously sidecast sediment mounds. This proposed installation would include dredging, plowing, backfilling, equipment anchoring, and anchor cable sweeping.
These activities would result in negative impacts to both the water quality and substrate. Turbidity of the water column would be relatively short-term. When this material precipitates out of the water column, it will result in sediment deposition on the benthic substrate. At the request of the Town of Branford’s Blue Ribbon Committee,30 John Roberge, P.E., LLC, prepared an assessment of sedimentation impacts associated with pipeline installation as modified by Islander East to mitigate sediment dispersion.31 The following sediment deposition pattern was estimated in Mr. Roberge’s study:
*1201 mm up to 100 meters from the trench centerline (approximately 70 acres); and
3 mm up to 40 meters from the trench centerline (approximately 35 acres).
The Department has determined that the negative impacts resulting from this depositional layer, in addition to direct substrate disturbance associated with dredging, plowing, backfilling, equipment anchoring, and anchor cable sweeping, are inconsistent with the Water Quality Standards. Pipeline installation would not only temporarily disturb water quality, it would permanently change the substrate and negatively impact the existing aquatic biota that depend on such substrate. The Connecticut Water Quality Standards define biological integrity as the ability of any aquatic ecosystem to support and maintain a balanced, integrated, adaptive community of organisms having a species composition, diversity, and functional organization comparable to that of the natural habitats of a region. The combined assaults of direct habitat disturbance and temporary water quality impacts resulting in sediment deposition negatively impact the overall biological integrity of the Thimbles [sic] Islands ecosystem and are therefore inconsistent with Standard No. 1 of the Connecticut Water Quality Standards.32
Pipeline installation through the Thimble Islands ecosystem will dramatically alter natural habitats and adversely impact the existing community of organisms. As discussed in a study entitled “Macrobenthic Community Structure Along The Proposed Islander East Pipeline Route In Long Island Sound,” by Pellegrino,33 there are dramatic differences in community structure associated with a disturbed versus a non-disturbed substrate. Once the original bottom has been disturbed, a soft sediment, referred to as the nephloide layer, covers the bottom and fills in any depressions left on the disturbed surface. Thus, the high-order or late successional stage species such as clams and oysters that lived in the original substrate can no longer exist. The community structure of the original substrate changes to that of early-stage opportunistic species such as polychaete worms. It is uncertain whether the associated diverse assemblage of bottom dwelling organisms currently present in this area could be reestablished. No studies exist from which one may predict a known recovery time for both these benthic communities and the substrate, if, indeed, there is any significant recovery.
Antidegradation Policy
Connecticut’s Water Quality Standards include an Anti-degradation policy34 as required by the Act (see Code of Federal Regulations, Title 40 Part 131.12). In brief, the policy requires that where water quality is better than the criteria established in the Water Quality Standards, such existing high quality must be maintained except under exceptional and very limited circumstances. In addition to addressing issues of quality, the policy mandates that existing uses must continue to *121be supported in all cases. Consistency with Connecticut’s Anti-degradation Policy and the procedures established in the Water Quality Standards to implement the policy is required for all activities regulated by the Department and can serve as the primary basis for Section 401 certification decisions.
As previously described, the pipeline is proposed to be sited within and adjacent to extensive shellfish grants, leased shellfish grounds and public shellfish lands. The discharge of backfill associated with pipeline installation would result in approximately 5.5 acres of nearshore bottom habitat being permanently degraded and rendered unsuitable for supporting the diverse assemblage of shellfish and other bottom dwelling organisms currently inhabiting this area. Because the bank-run gravel would also interfere with harvesting techniques, the area of impact to shellfish harvesting would extend well beyond the 5.5 acres of direct disturbance. While the gravel-filled trench would be 37' wide, the area that the commercial shellfish harvesting equipment would need to avoid would be much wider because of the required turning radius of the vessels with gear in tow.
Additionally, the resulting topographic irregularities over the entire 3,700-acre Islander East corridor caused by sedimentation, backfill with gravel, plow utilization, anchor strikes, and cable sweeps will adversely affect the population of resident benthic organisms and shellfish as well as the efficiency and safety of the existing shellfish harvesting operations and handling of shellfish harvesting equipment. The application materials indicate that it is the goal of the applicant to achieve a finished substrate equivalent to the adjacent benthic surface with a proposed acceptable tolerance of +2' to -1'. Based on the experience of the Department with the installation of the Iroquois pipeline in 1991, the Department does not agree that such a minimal impact restoration of the work site contours can, in practice, be achieved. While such a range in tolerance level might be less significant in an area of lower environmental value, where shellfish resources were scarce due to lack of suitable habitat, or where traditional harvest shellfishing techniques were not employed, that is not the case in respect to the area through which the pipeline route has been proposed by Islander East.
Summary
The Department therefore finds that Islander East’s proposed work is inconsistent with Connecticut’s federally-approved Water Quality Standards. Due to the sensitive nature of the receiving waters and the ecological system dependent upon such water, the Department has determined that the regulated activity in the proposed location will permanently alter the existing high quality physical and biological integrity and productivity of this area to the extent that the existing uses for habitat for marine fish, other aquatic life and wildlife and shellfish harvesting for direct human consumption will be impaired. Essential shellfish habitat will be lost due to the temporary and permanent alteration of the benthic environment resulting from the proposed work. Finally, the siting of the non-water dependent pipeline through prime shellfish habitat would cause a significant and permanent adverse impact to a water-dependent use by displacing the water-dependent use of shellfishing with the non-water-dependent use of natural gas transmission.
. See Appendix A. State of Connecticut, Department of Environmental Protection, Water Quality Standards.
. Initiated in 1985, the Long Island Sound Study (LISS) is a partnership of federal, state, and local governments [sic] agencies, private organizations and citizens formed to develop and implement a comprehensive conservation and management plan for Long Island Sound. Funding support for the LISS is provided by the Environmental Protection Agency through *118the National Estuary Program and by the States of Connecticut and New York.
. See Appendix B for summary of monitoring program and survey results.
. See Appendix C for map of Water Quality Classification areas.
. Please refer to Appendix A (Water Quality Standards, pages 15-17) for a more complete description of these classifications and designated uses.
.Northeast Coastal Areas Study: Significant Coastal Habitats of Southern New England and Portions of Long Island, New York (August, 1991). The United States National Marine Fisheries Service has also designated Long Island Sound as an "Essential Fish Habitat (EFH)."
. MSX (multinucleated sphere unknown) is a single-cell parasite that invades the oyster's soft body, grows and divides within the tissue, and eventually overwhelms the normal metabolic processes in the shellfish resulting in death.
. Statistics provided by Kelly Streich, DEP Water Bureau[.]
. A committee appointed by the Town of Branford First Selectman to review and comment on the Islander East application.
. See Appendix E for report dated May 5, 2003 with September 30, 2003 and February 4, 2004 amendments.
. Surface Water Quality Standard No. 1 — It is the State’s goal to restore or maintain the chemical, physical, and biological integrity of surface waters. Where attainable, the level of water quality that provides for the protection and propagation of fish, shellfish, and wildlife and recreation in and on the water shall be achieved.
. Appendix F, Final Report, January 2002, section 4.0.
. See Appendix A, Water Quality Standards. The Connecticut Anti-degradation Implementation Policy is found in Appendix E of Water Quality Standards.