While spatial heterogeneity of riverine nitrogen (N) loading is predominantly driven by the magnitude of basin‐wide anthropogenic N input, the temporal dynamics of N loading are closely related to the amount and timing of precipitation. However, existing studies do not disentangle the contributions of heavy precipitation versus non‐heavy precipitation predicted by future climate scenarios. Here, we explore the potential responses of N loading from the Mississippi Atchafalaya River Basin to precipitation changes using a well‐calibrated hydro‐ecological model and Coupled Model Intercomparison Project Phase 5 climate projections under two representative concentration pathway (RCP) scenarios. With present agricultural production and management practices, N loading could increase up to 30% by the end of the 21st century under future climate scenarios, half of which would be driven by heavy precipitation. Particularly, the RCP8.5 scenario, in which heavy precipitation and drought events become more frequent, would increase N loading disproportionately to projected increases in river discharge. N loading in spring would contribute 41% and 51% of annual N loading increase under the RCP4.5 and RCP8.5 scenarios, respectively, most of which is related to higher N yield due to increases in heavy precipitation. Anthropogenic N inputs would be increasingly susceptible to leaching loss in the Midwest and the Mississippi Alluvial Plain regions. Our results imply that future climate change alone, including more frequent and intense precipitation extremes, would increase N loading and intensify the eutrophication of the Gulf of Mexico over this coming century. More effective nutrient management interventions are needed to reverse this trend.