Issuance of a permit conditioned on obtaining of second state permit did not offend the Act, as the conditional permit did not allow any discharges into the waters of the United States.
As each project is viable without the other, agency was not arbitrary or capricious in considering them separately.
Deference to agency determination that nonjurisdictional utility project was not sufficiently connected to jurisdictional projects to warrant formal review.
Agency's determination of minimal impacts appropriately resolved claim of cumulative impacts.
etc, etc. ...
Original federal appellate jurisdiction for violations of the act does not displace state administrative remedies in the permitting process.
http://www2.ca3.uscourts.gov/opinarch/171047p.pdf
Since 2011. An occasional commonplacing of the U.S. Circuit Courts of Appeal.
Neither an authoritative statement of the law nor legal advice. Quick work.