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River-estuary continuums represent a dynamic range of environmental conditions in aquatic ecosystems, providing an ideal gradient for understanding changes in nitrogen (N) cycling. We measured rates of ammonium (NH4 (+)) cycling, including uptake and regeneration, in the water column of upper river, lower river, and estuary sites. This 1-year study encompassed periods of flood and drought, in a coastal catchment of south Texas. Low NH4 (+) concentrations and frequently balanced net NH4 (+) fluxes suggest minimal N cycling, but these measurements alone did not reveal the patterns of water column NH4 (+) uptake and regeneration in the river and estuarine systems. Rapid turnover of NH4 (+) supported productive estuaries, particularly during periods of droughts when riverine sources of NH4 (+) were minimal. However, NH4 (+) demand declined during storms across the river-estuary continuum, and regeneration rates were high, especially in the rivers. Most research in rivers has focused on benthic or whole-system dynamics, but our data demonstrate that active NH4 (+) cycling also occurs in isolated river water columns. Lower river sites were hotspots of NH4 (+) cycling on the landscape. Continued studies across river-estuary continuums are needed to enhance our understanding of aquatic systems and improve our ability to manage nutrients in the face of increased anthropogenic pressures and a changing climate.