N.Y. Comp. Codes R. & Regs. tit. 6, § 815.4 – Special conditions.

(a) All streams and 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, 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 indicaed in table I and the aforementioned special conditions statements, 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 Environmental 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 1260 of article 12 of the Public Health Law provides that the Water Pollution Control Law shall not abridge or alter rights of other authorities such as provided by watershed rules and regulations.
1. (1) In regard to adoption of classifications and standards of water quality under article 12 of the Pubic Health 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 Water Resources Commission 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 12 of the Public Health 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 Water Supply, Gas and Electricity, as approved by the State Commissioner of Health, will apply in accordance with law, and the adoption of the classifications herein by the Water Resources Commission and the enforcement thereof by the State Commissioner of Health 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 Water Supply, Gas and Electricity.