N.Y. Comp. Codes R. & Regs. tit. 6, § 879.4 – Special conditions.

(a) All streams or other bodies of water which appear as lines to indicate natural waters on the reference maps herein, and which are not specifically designated in table I, shall be assigned the same classes and standards of quality and purity as the specifically designated waters to which they are directly tributary.
(b) All streams or other bodies of water which are not shown on the reference maps herein shall be assigned to class D, as set forth in Part 701, supra, except that any continuous flowing natural stream which is not shown on the reference maps shall have the same classification and assigned standards as the waters to which it is directly tributary.
(c) Notwithstanding the items indicated in table I and the aforementioned special conditions, (a) and (b), which, in some instances, may indicate assignment of other than class A to streams tributary to New York City water supply impoundments within lands owned by New York City, such waters within the boundaries of lands owned by New York City shall be assigned to class A with standards of quality and purity for class A.
(d) Notwithstanding the items indicated in table I and the aforementioned special conditions statements which, in some instances, may indicate assignment of classifications for waters contained within the boundaries of the State-owned forest preserve lands and, therefore, controlled under the provisions of the State Constitution and the Conservation Law, such waters are hereby excluded from classification to the extent that any part of such waters may be located within the boundaries of the State-owned forest preserve lands. All waters within 100 feet of the boundaries of the State-owned forest preserve lands shall be assigned to class A with standards of quality and purity for class A.
(e) Section 17-1105 of the Environmental Conservation Law provides that conflicting laws regarding water pollution control shall be ancillary to and supplement the Environmental Conservation Law, except if they are in direct conflict. Accordingly, the watershed rules and regulations promulgated to protect certain water supply areas shall not be abridged or altered.
1. (1) In regard to adoption of classifications and standards of water quality under article 17 of the Environmental Conservation Law, and in the enforcement of the provisions of such article, it is recognized that any rules and regulations either made or promulgated by the Department of Health under article 11 of the Public Health Law for the protection from contamination of public water supplies, will apply in accordance with law, and the adoption of classifications by the Department of Environmental Conservation herein shall in no manner limit the protection of waters afforded by said rules and regulations.
2. (2) In regard to adoption and enforcement of classifications and standards of water quality under article 17 of the Environmental Conservation Law for waters tributary to New York City water supplies, it is recognized that any rules and regulations of the New York City Board of Water Supply and the Department of Environmental Protection, as approved by the State Commissioner of Health, will apply in accordance with law, and the adoption of the classifications herein by the Department of Environmental Conservation and the enforcement thereof by the State Commissioner of Environmental Conservation in no manner shall limit or lessen or abridge the protection afforded by said rules and regulations of the New York City Board of Water Supply and Department of Environmental Protection.