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Nissequogue () is a village in Suffolk County, New York, United States, on the North Shore of Long Island. As of the 2010 census, the village population was 1,749.
The village of Nissequogue is located in the town of Smithtown. It is within the postal boundaries of the St. James, New York, but it is not part of St. James. It became an incorporated village in 1926.
The current mayor of the village is a descendant and a namesake of the first English settler of the village, Richard Smith (Smythe).
According to the United States Census Bureau, the village has a total area of 4.0 square miles (10 km2), of which 3.8 square miles (9.8 km2) is land and 0.2 square miles (0.52 km2), or 5.04%, is water.
To the west of the village is its namesake, the Nissequogue River. To the north is Long Island Sound, while to the east is Stony Brook Harbor. Moriches Road runs through the center of the village.