Jefferson County is a county located in the U.S. state of New York. As of the 2010 census, the population was 116,229. It is named after Thomas Jefferson, third President of the United States of America, and president at the time the county was created in 1805. Its county seat is Watertown. It is adjacent to Lake Ontario, southeast from the Canadian border of Ontario.

Jefferson County is in northeastern New York State, adjacent to the area where the Saint Lawrence River exits Lake Ontario. It is northeast of Syracuse, and northwest of Utica. The county is at the international border with Canada.

The Black River, which empties into Lake Ontario, is an important waterway in the county. Part of the Tug Hill Plateau is in the southern part of the county.

The county also includes nearby islands in the St. Lawrence River, including such large islands as Carleton Island, Grindstone Island, and Wellesley Island.