The City of Ithaca's produces the Six Mile Creek watershed website which is focused on water treatment and distribution in the region.
The waterbodies section of the New York Department of Environmental Conservation website provides information on watersheds, wetlands, groundwater and more. Their site also includes interactive maps.
How's My Waterway is an EPA website (migrated from the previous (Surf Your Watershed) that allows you to drill down from the national to state to local level in terms of water quality data for watersheds. Additional resources are posted on EPA's Water Data and Tools page.
The United States Geologic Survey (USGS) supports the National Water Information Center -- a data repository built in local water quality analyses.
Facts on Cayuga Lake compiled by the New York DEC.
NYFalls provides an index to New York state waterfalls.