The creek's valley is mostly low-lying level land, with the exception of the area above its headwaters in Union Vale. Most of its descent takes place either in its uppermost 10 miles (16 km), above Poughquag, or its lowermost 5 miles (8 km), below the village of Fishkill, both stretches of which account for each of its total drop. The average elevation within the watershed is above sea level. To the south and east are hiller regions of the Taconic Mountains, part of the Highlands Province physiographic region of the Appalachian Mountains. The highest point in the Fishkill's watershed is South Beacon Mountain, also the highest peak of the Hudson Highlands, a few miles from the creek's estuary, which is almost at sea level. In Union Vale, near the creek's source, Clove Mountain rises to .