High concentrations of naturally occurring arsenic (As) are typically found in young alluvial and deltaic deposits, and high concentrations of ammonium (NH4+) and nitrate (NO3-) are often present in groundwater affected by anthropogenic activities. In this study, on the basis of physicochemical characteristics of groundwater and the nitrogen and oxygen isotope composition of NO3-, it was inferred that the main sources of NO3- in the proximal fan of the Choushui River alluvial fan are likely to be ammonium fertilizers, manure, and septic waste; that in the mid-fan and the distal fan, the possible sources are nitrate fertilizers and marine nitrate. In the proximal fan, the oxidative state obviously promotes microbial nitrification. Denitrification occurs from the upstream region to the downstream region of the Choushui River, and therefore, the decrease in NO3- concentration along streams connecting the Choushui River to the ocean appears plausible. High DO concentrations and relatively low values of δ18ONO3 in the deeper aquifer of the proximal fan may be attributed to unconfined granular nature and groundwater pumping by agricultural activities. In the mid-fan, NO3- assimilation is the dominant response to NO3- attenuation, and denitrification is insignificant; however, high concentrations of As, NH4+ and Fe and depletion of δ15NNO3 imply the occurrence of feammox process. By contrast, denitrification evidently occurs in the distal fan, through assimilation, mineralization, and dissimilatory NO3- reduction to NH4+, resulting in depletion of NO3- and increase in NH4+ in groundwater. Feammox in the mid-fan and denitrification in the distal fan may be the main processes leading to the release of As from As-bearing Fe oxyhydroxides into groundwater.