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Abstract The seasonal controls of hydrology, temperature, hypoxia, and biogeochemical conditions for groundwater ammonium–N (NH₄⁺) concentrations are not well understood. Here we investigated these controls for riparian groundwaters located upstream of two milldams over a period of 4 years. Groundwater chemistry was sampled monthly while groundwater elevations, hydraulic gradients, and temperatures were recorded sub‐hourly. Distinct seasonal patterns for NH₄⁺were observed which differed among the wells. For wells that displayed a strong seasonal pattern, NH₄⁺concentrations increased through the summer and peaked in October–November. These elevated concentrations were attributed to ammonification, suppression of nitrification, and/or dissimilatory nitrate reduction to ammonium (DNRA). These processes were driven by high groundwater temperatures, low hydraulic gradients (or long residence times), hypoxic/anoxic groundwater conditions, and increased availability of dissolved organic carbon as an electron donor. In contrast, NH₄⁺concentrations decreased in the riparian groundwater from January to April during cool and wet conditions. A groundwater well with elevated total dissolved iron (TdFe) concentrations had elevated NH₄⁺concentrations but displayed a muted seasonal response. In addition to hydrologic controls, we attributed this response to additional NH₄⁺contribution from Fe‐driven autotrophic DNRA and/or ammonification linked to dissimilatory Fe reduction. Understanding the temporal patterns and factors controlling NH₄⁺in riparian groundwaters is important for making appropriate watershed management decisions and implementing appropriate best management practices.