N.Y. Comp. Codes R. & Regs. tit. 6, § 750-2.2 – Exclusions.

(a) The issuance of a SPDES permit by the department and the receipt thereof by the applicant does not supersede, revoke or rescind an order on consent or modification thereof or any of the terms, conditions or requirements contained in such order or modification thereof unless specifically intended by said order or a newly issued order.
(b) The issuance of a SPDES permit does not convey any property rights in either real or personal property, or any exclusive privileges, nor does it authorize any injury to private property or any invasion of personal rights, nor any infringement of Federal, State or local laws or regulations; nor does it obviate the necessity of obtaining the assent of any other jurisdiction as required by law for the discharge authorized.
(c) A SPDES permit does not authorize or approve the construction of any onshore or offshore physical structures or facilities or the undertaking of any work in any navigable waters.
(d) Oil and hazardous substance liability.
The imposition of responsibilities upon, or the institution of any legal action against the permittee under section 311 of the act (see section 750-1.25 of this Part) shall be in conformance with regulations promulgated pursuant to section 311 governing the applicability of section 311 of the Clean Water Act to discharges from facilities with NPDES permits.