One of New York Sea Grant's main focus areas in the New York City region for research, extension and education efforts is the Hudson River, which flows through 315 miles of eastern New York from the Adirondack Mountains. The lower half of the Hudson is an estuary influenced by ocean tides and saltwater. Bordered by 15 New York State counties, the estuary is defined by the Federal Dam at Troy and the Verrazano Narrows in New York City.

Some New York Sea Grant research also takes place in and around the New York - New Jersey Harbor Estuary. The estuary opens into the New York Bight and Long Island Sound, the latter of which is also a main focus area for New York Sea Grant (see NYSG's related news).

The Long Island Sound Study, conducted under the Environmental Protection Agency’s National Estuary Program, is a cooperative effort between the EPA and the states of Connecticut and New York to restore and protect the Sound and its ecosystems.

NYSG also has a partnership with the Science and Resilience Institute at Jamaica Bay that focuses on that estuary.