Water management to protect agriculture in alluvial floodplains often conflicts with wildlife use of seasonal floodwater. Such is the case along the Mississippi River in southeastern Missouri where migrating shorebirds forage in shallow-flooded fields. I estimated the current availability of habitat for foraging shorebirds within the New Madrid and St. Johns Basins based on daily river elevations (1943–2009), under assumptions that shorebirds forage in open habitat with water depth <15 cm and use mudflats for 3 days after exposure. The area of shorebird foraging habitat, based on replicated 50-year random samples, averaged 975 ha per day during spring and 33 ha per day during fall. Adjustments to account for habitat quality associated with different water depths, duration of mudflat exposure, intra-seasonal availability, and state of agricultural crops, indicated the equivalent of 494 ha daily of optimal habitat during spring and 11 ha during fall. Proposed levees and pumps to protect cropland would reduce shorebird foraging habitat by 80 %: to 211 ha (108 optimal ha) per day during spring and 9 ha (<3 optimal ha) per day during fall. Alternative water management that allows natural flooding below a prescribed elevation would retain nearly all existing shorebird foraging habitat during fall and about 60 % of extant habitat during spring.