Fishkill Creek is a tributary of the Hudson River in Dutchess County, New York, United States. At 33.5 miles (53.9 km) it is the second longest stream in the county, after Wappinger Creek. It rises in the town of Union Vale and flows generally southwest to a small estuary on the Hudson just south of Beacon. Part of its 193-square-mile (500 km2) watershed is in Putnam County to the south. Sprout Creek, the county's third-longest creek, is its most significant tributary. Whaley and Sylvan lakes and Beacon Reservoir, its largest, deepest and highest lakes, are among the bodies of water within the watershed.