The long‐term evolution of nutrient dynamics in rivers under changing external forcings, termed hereafter trajectory, is influenced by local human activities and regional climatic variations. Here we investigate nitrogen (N) and phosphorus (P) dynamics in seven mesoscale agricultural catchments (median size 800 km2) of western France from seasonal to multidecadal time scales (1970–2016). Results show that, in these catchments dominated by shallow groundwater, long‐term nitrate exports responded to variations of the agricultural N surplus with time lags of approximately 10 years. Presence of legacy N storage, related to the catchments' denitrification capacity, was found to increase response times. In contrast, P trends were predominantly controlled by decreasing point source emissions during the study period, and P dynamics were influenced by in‐stream retention/remobilization processes that hampered precise quantification of land‐to‐river diffuse transport processes. Occurrence of interannual climate variations during three 5‐ to 10‐year dry‐wet cycles, influenced by the North Atlantic Oscillation, affected N and P dynamics with persistent interannual hysteresis patterns among catchment and years. Thus, water quality assessment programs should cover at least five years to decipher the effect of mitigation measures from climate variations. Key Points Long‐term N and P trends disentangled from effect of interannual climate variability N and P trends responded to changes in agricultural N surplus and point source P inputs, respectively Time lags in N load response to variations in inputs influenced by legacy storage in catchments