Freshwater flow is generally held to be one of the most influential factors affecting community structure and production in estuaries. In coastal Louisiana, the Caernarvon Freshwater Diversion (CFD) is managed to control freshwater discharge from the Mississippi River into Breton Sound basin. Operational since 1991, CFD has undergone several changes in management strategy including pulsed spring flooding, which was introduced in 2001. We used a 20-yr time series of fisheries-independent data to investigate how variation in freshwater inflow (i.e., pre- and post-CFD, and pre and post spring pulsing management) influences the downstream nekton community (abundance, diversity, and assemblage). Analyses of long-term data demonstrated that while there were effects from the CFD, they largely involved subtle changes in community structure. Spatially, effects were largely limited to the sites immediately downstream of the diversion and extended only occasionally to more down-estuary sites. Temporally, effects were 1) immediate (detected during spring diversion events) or 2) delayed (detected several months post-diversion). Analysis of river management found that pulsed spring-time inflow resulted in more significant changes in nekton assemblages, likely due to higher discharge rates that 1) increased marsh flooding, thus increasing marsh habitat accessibility for small resident marsh species, and 2) reduced salinity, possibly causing displacement of marine pelagic species down estuary. ?? 2010.