New York is near the northern limit of the Black Skimmer's breeding range, with breeding populations being restricted to beaches, dredge spoil islands, sandy non-barrier islands, and recently, salt marsh islands along the coast of southern Long Island (New York Natural Heritage Program 2009). Much of the former breeding habitat has been lost due to development and recreational activities along Long Island's beaches, resulting in the Black Skimmer and other beach-nesting species to nest on salt marsh islands (Gochfeld and Burger 1994; McGowen and Corwin 2008).

Black Skimmer populations in New York appear to be variable, with some degree of yearly fluctuation due to the timing of formal survey periods. The first Breeding Bird Atlas (1980-1985) had confirmed breeding Black Skimmers in 23 blocks mostly along the southern shore of Long Island. The second Atlas (2000-2005) saw reduced numbers of skimmers with confirmed breeding in 18 blocks, again, mostly along southern Long Island (McGowen and Corwin 2008). Black Skimmers are surveyed annually and over the last eight years, their numbers have ranged from a low of 265 in 2004 to a high of 622 in 2008 with an average of 445 pairs (Gibbons 2008). These numbers may be slightly low as Black Skimmers nest later in the season than the June survey period and numbers for the peak nesting season may be missed. About 16 out of 49 colonies are still active (New York Natural Heritage Program 2009).

Black Skimmers have been seen in New York since the mid 1800s (Gochfeld and Burger 1994). They were first discovered breeding on Long Island in 1934 at Gilgo State Park (Vogt 1934). They were common breeders on Long Island throughout the middle of the 20th century, with an average of over 400 pairs at 10-13 colonies reported during surveys conducted from 1974-1978 (Buckley and Buckley 1980).