The historical ecological state of the Mississippi Alluvial Plain (MAP) was a vast bottomland hardwood forest with seasonal widespread inundation from the Mississippi River. Today the MAP is an extensive, highly productive, row-crop agricultural region that is protected from flooding by significant hydromodification. The MAP and other similar modern agroecosystems represent coerced complex adaptive systems with uncertain ecological resilience due to their relatively new ecological condition. While quantitative measures of resilience for highly modified agroecosystems are elusive, finding ways to insert biogeochemical function provided by wetlands back into agroecosystems is key to maintaining dynamic ecological landscapes that enhance availability of clean water and provide habitat for wildlife, all while maintaining productive agricultural activities. We are working with farmers to evaluate how post-harvest flooding for migratory shorebird habitat influences nutrient biogeochemistry in row-crop fields across a portion of the MAP. Our observations demonstrate that flooding fields in the fall support the rapid buildup of benthic macroinvertebrate densities that provide a stopover food resource for migratory shorebirds. Flooding after corn harvest resulted in net denitrification rates that were sustained throughout the inundation period and culminated in an estimated 33-45 kg ha-1 of excess N removed. Lower denitrification benefits were associated with flooding soybean fields compared to corn fields. Flooding reduces soil nitrate (NO3-N) while increasing soil ammonium (NO4-N) over time in corn and soybean fields. Flooding also led to reductions in mean storm event runoff concentrations for suspended solids, NO3-N, phosphate (PO4-P), and total phosphorus (P). Comparisons of soil nutrients pre- and post-flooding indicated that flooding led to lower plant available P in soils, but the degree of this reduction was relatively minor, and was only observed in fields flooded for the entire fall-winter sequence. No yield impacts attributed to managed flooding for migratory shorebird habitat have been reported by 10 different participating farmers across 19 locations. Our results suggest that novel timing of shallow water habitat management provides temporary wetland structure and biogeochemical function that can provide critical shorebird habitat and support downstream water quality benefits, without impacting crop yields within MAP agroecosystems.