Floodplains of large rivers are exploited for agricultural production, industrial and municipal development, and transportation infrastructure. Recently, increased frequency of costly floods has prompted consideration of whether offsetting benefits might accrue from management of floodplains for ecosystem services. We employed a simple inundation model for 800 km of the Lower Missouri River, USA, to evaluate spatial and temporal distributions of ecological floodplain inundation metrics and how those distributions might vary with levee removal and climatic change. The model evaluates inundation at 30 × 30 m resolution on a daily basis over 82 years of record. We quantified provisioning of waterfowl habitat and potential denitrification. Spatial variability is affected by ongoing geomorphic adjustments that affect floodplain connectivity. Statistical models indicate that available floodplain area and recent aggradation are predictive of most inundation metrics. Connectivity is sensitive to climate-change scenarios that predict increased floodplain inundation during spring waterfowl migrations; the greatest sensitivity to future climate exists where channel-floodplain geomorphology presently enhances floodplain connectivity. Evaluation of floodplain denitrification indicates that on average, the nonleveed part of the floodplain could denitrify 0.05%–1.7% of the mean annual nitrogen load of the river. Levee removal could increase this rate to only 3.6% of the nitrogen load. The capacity of floodplain connectivity to influence certain ecosystem services is highly variable in space along the Lower Missouri River and may be appreciably influenced by climate change. Hence, decisions to optimize management of large-river floodplains are likely to be highly location dependent.