Petersburg National Battlefield is located within two drainage basins (Chesapeake Bay and Albermarle Sound). The confluence of the James and Appomattox Rivers occurs at City Point, and, because of the James' eventual outlet into the Chesapeake Bay, the park is included in the Virginia Coastal Zone.

Five streams drain the Eastern Front, and they are all within the Chesapeake Bay drainage basin. Poor and Harrison Creeks are the largest. Taylor's Creek is a tributary of Poor Creek, and Branch Creek and an unnamed creek are tributaries of Harrison Creek. All of these creeks drain into the Appomattox River, and, after that, into the Chesapeake Bay.

The park's Western Front lies in Dinwiddie County. This site is drained by Rohoic Creek, which eventually empties into the Appomattox River. Five Forks is drained by Hatcher's Run and Chamberlain's Bed Creek. These creeks drain into the Nottoway River, which drains into the Chowan River, and ultimately reach the Atlantic Ocean.