Coastal aquifers are host to a range of biogeochemical reactions that alter groundwater‐derived nutrient, metal, and other chemical loads to coastal ecosystems. Temperature is a strong control on microbially mediated reactions; thus, chemical reactivity in coastal aquifers may vary spatially and temporally with changes to groundwater temperature. In this study, we investigated the influence of global groundwater and sea surface temperature controls and seasonal temperature variability on biogeochemical processing in coastal aquifers using variable‐density groundwater flow, heat transport, and reactive transport models. The coupled models showed that nitrate removal efficiency in coastal aquifers increased from 5% to 88% as fresh groundwater temperature increased from 5°C to 35°C, while ocean temperature had a negligible effect on removal efficiency. Transient simulations based on monthly groundwater and ocean temperature measurements showed that denitrification and ammonification hotspots migrated seaward seasonally within warm fresh groundwater masses. The reaction hotspots were separated by colder groundwater emplaced during winter months. The reaction hotspots and nitrate plumes oscillated vertically along horizontal flow paths due to buoyancy effects between warm and cold groundwater. Comparison between transient and temperature‐equivalent steady‐state models suggests that steady‐state models adequately capture mean annual NO₃⁻ removal, but neglect local reactive transience and changes to plume geometry. The sensitivity analysis provides a first‐order estimate of the reactive potential of coastal aquifers considering globally diverse thermal regimes. The findings have implications for regional‐scale estimates of groundwater nutrient fluxes and for predicting coastal aquifer reactivity in a warming climate.