Excess nitrogen (N) from anthropogenic sources deteriorates freshwater resources. Actions taken to reduce N inputs to the biosphere often show no or only delayed effects in receiving surface waters hinting at large legacy N stores built up in the catchments soils and groundwater. Here, we quantify transport and retention of N in 238 Western European catchments by analyzing a unique data set of long-term N input and output time series. We find that half of the catchments exhibited peak transport times larger than five years with longer times being evident in catchments with high potential evapotranspiration and low precipitation seasonality. On average the catchments retained 72% of the N from diffuse sources with retention efficiency being specifically high in catchments with low discharge and thick, unconsolidated aquifers. The estimated transport time scales do not explain the observed N retention, suggesting a dominant role of biogeochemical legacy in the catchments’ soils rather than a legacy store in the groundwater. Future water quality management should account for the accumulated biogeochemical N legacy to avoid long-term leaching and water quality deteriorations for decades to come.