Excluding the bluffs along the periphery of the Refuge, elevation across the Mingo Basin varies less than 10 feet, rising from 335 to 344 feet above mean sea level. Minor changes in water levels result in vast differences in amount of area flooded. Four green tree reservoirs totaling 3,721 acres and two open marsh impoundments totaling 3,305 acres are managed for waterfowl and other wetland associated wildlife through water level manipulation.

Nearly 60 miles of ditches and over 57 water control structures form a drainage network that moves 45 billion gallons (137,740 acre feet) of water annually onto, around, and off the Refuge. These ditches hold water year-round and often provide refuge for fish species during low water periods. Actions to improve water transport throughout the ditch network reduce flood duration and improve bottomland forest dynamics, helping meet the Refuge purpose of providing habitat for migratory birds.

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