The water level of tidally connected saltwater ponds may be adjusted via water control structures using different techniques dependent upon management objectives (i.e., fishing, wading birds, diversity, recruitment, etc.). Riser-board water control structures will have only infrequent water exchange. Water control structures with flap gates that allow water to enter the pond when tide levels on the outside are higher than water levels inside the pond. Incoming water brings baitfish, crustaceans and zooplankton. Increased water flow also increases oxygen levels in the pond. While rice trunks are a common water control structure in the ACE Basin, the high salinity of Port Royal Sound degrades the wood quickly, so the Trust has utilized an aluminum structure in the Great Salt Pond.

Fish kills can occur in warm, shallow saltwater impoundments when a heavy summer rainfall causes oxygen-deprived water from the bottom of the pond to rise to the surface. An aerator can increase dissolved oxygen in the water.