Whenever quailty of water or improvements to water are a factor, The NYSDEC are first ones on the scence. The New York State Department of Environmental Conservation provides funding for projects to improve water quality through the Water Quality Improvement Project (WQIP) Statewide Grant Program. The WQIP Program provides funding through the New York State Environmental Protection Fund (EPF) for projects demonstrating direct environmental benefits that will help reduce polluted runoff, improve water quality and restore habitat in New York State waters. 

Eligible applicants for the program are, Municipalities, Soil and Water Conservation Districts. 

There several types of projects eligible for funding, which are used to focus efforts on specific water quality issues. Several of the project types have sub-categories. The five (5) basic types are, Municipal Wastewater Treatment, Municipal Separate Storm Sewer Systems (MS4s), Nonagricultural Nonpoint Source Abatement and Control, Aquatic Habitat Restoration, Water Quality Management and Depending on the type of project, funding recipients can be reimbursed for up to 85% of the total cost of the project.

http://www.dec.ny.gov/pubs/4774.html