The Atchafalaya River Basin Floodway (ARBF), a regulated river/floodplain distributary of the Mississippi River, experiences an annual flood pulse that strongly influences floodplain physicochemistry. We developed several metrics to investigate the relationship between the timing and magnitude of the flood pulse and floodplain hypoxia, which in most years is a spatially extensive and temporally prolonged problem in the lower ARBF. Principal components analysis of flood metrics from 2001 to 2009 revealed contrasting flood types (early cool and late warm), but component‐based general linear models were unable to predict the magnitude of hypoxia in ARBF water management areas (WMAs). Further analyses based on temperature and geographic information system‐determined WMA inundation with generalized additive models (GAMs) revealed WMA‐specific patterns of hypoxia, but the likelihood of hypoxia consistently increased when temperatures approached 20°C and inundation rose above 20–30%. Validation with held‐out data based on logistic regression indicated that the models constructed with the 2001–2009 temperature and inundation data were able to accurately predict the probabilities of hypoxia in two WMAs based on data collected from 2010 to 2013. The GAMs were an effective tool for visualizing and predicting the probability of hypoxia based on two easily generated parameters. Our analyses indicate that modification of the Atchafalaya River flood pulse could reduce the magnitude of hypoxia within the lower ARBF, subject to engineering (control structure operation) and economic (commercial fisheries production) constraints, by minimizing floodplain inundation after water temperatures reach 20°C. Copyright © 2015 John Wiley & Sons, Ltd.

Little is known about water movement, volume, or residence time (RT), and how those characteristics affect sediment trapping efficiency (TE) and dissolved oxygen concentrations (DO) in the United States' largest remaining bottomland hardwood swamp, the Atchafalaya River Basin. To better understand these dynamics, this study used bathymetry, lidar, and stage records to determine volumes in the Basin's hydrologically distinct water management units (WMUs). Discharge measurements determined flow distribution and RT. Residence time was compared with DO to identify conditions that coincided with DO increases or decreases. Suspended sediment concentrations (SSC) were used to determine TE relative to calculated and measured discharge and RT. Discharge through units (85–2,200 m3/s) and RT (0.37–231 d) depended on connectivity and river stage. At high stages, with water temperatures >20°C, DO in the largest WMU declined by −0.21 mg/l/day. DO trends indicated less well‐connected areas of the WMU contributed hypoxic waters as the flood wave lengthened and stages fell. In the two WMUs examined for TE, TE (−266% to 99% and up to 38 Gg/day) correlated with hydrologic connectivity, SSC, RT, water volume, and, in one WMU, discharge losses. Long RT and high TE indicated a high potential to process nutrients. These relationships varied among WMUs. Large volumes of sediment‐laden water moving over the floodplain combined with long RT, high TE, and hypoxia indicate that this ecosystem has continental‐scale importance in reducing nutrient loads to the northern Gulf of Mexico. Reports from other systems suggest similar processes may be operating on other large river floodplains globally.