The tidal portion of Darby Creek and its side channels flows through the refuge and tidal marsh. Streams are important corridors for fish and wildlife migration. The biological habitat in the immediate vicinity of a stream is called a riparian zone which provides wildlife habitat for a diversity of species, shade to help regulate water temperature changes, and an erosion buffer to absorb impacts of increased runoff from urban development. Darby Creek is known to support a diversity of estuarine fish species such as killifish and mummichogs. Anadromous fish, such as the blueback herring and alewife, use tidal streams and rivers like Darby Creek and its side channels as nursery habitat for juveniles. American eel, the only catadromous fish species in Atlantic Coast estuaries, spends most of its adult life in freshwater and are common in tidal creeks, rivers, and marsh channels. Waterfowl like the American black duck, lesser scaup, and northern pintail as well as shorebirds like black-bellied plover, greater yellowlegs, and semipalmated sandpiper also utilize open water habitats along Darby Creek for migratory stopovers.
The water quality at the refuge is determined by the combination of waters from Darby Creek, Cobbs Creek, and the Delaware River. Philadelphia Water Department and other local, regional, and State agencies have conducted a series of watershed assessments and water quality characterizations that have detailed the water quality impacts related to urbanization and other watershed impacts. Other smaller streams (such as Muckinipattis and Hermesprota Creeks) directly connected to the refuge may also pose important considerations for water quality. Many water quality issues are watershed-scale concerns.