Fishkill Creek's watershed is the second largest in Dutchess County after Wappinger Creek to the north. It includes almost the entire towns of Beekman and Union Vale, large portions of East Fishkill and Fishkill, sections of LaGrange and Wappinger and small areas in Pleasant Valley and Washington. The Whaley Lake basin, which also includes Little Whaley and Nuclear lakes, is in Pawling. In Putnam County the largest town represented is Philipstown, whose northwestern section (the Clove Creek watershed) drains into the Fishkill. A small portion is in Kent, with an even smaller portion in Putnam Valley marking the watershed's southernmost point.