<p>The land along the coast is often hydrologically disconnected from the prevailing river systems. Water flow and nutrient transport from these disconnected coastal subcatchments follow diffusive pathways and can hardly be quantified. Therefore, it is unknown, to what extent coastal waters might be affected by diffuse nutrient inputs. Here, we develop a GIS-based method to derive hydraulic heads and gradients (groundwater) in coastal subcatchments aiming at estimating the pollution risk of the coastal seas with nutrients originating from agricultural activity. The nutrient export risk from the land was defined as the product of hydraulic gradient (groundwater), agricultural density and the subsoil saturated hydraulic conductivity. The developed method is applied to the Southern Baltic Sea coast of the Federal State of Mecklenburg–Western Pomerania in northeastern Germany. Our results indicate that subsurface export of dissolved nutrients plays an important role in controlling nutrient fluxes into the sea. Furthermore, subcatchment nutrient export risk generally increases from the east to the west with a few exceptions such as those surrounding the Rügen Lagoon, where high nutrient export risk calculated as a result of steep hydraulic gradients, coincides with high nutrient concentrations reported for its limnic-marine transitional waters. The presented method has a good potential to be further developed by including meteorological and hydrogeological data. In the absence of data on nutrient export via diffusive pathways to the Baltic Sea, spatial risk mapping from disconnected subcatchments provides a rapid approach to identify ‘at-risk’ catchments. This can help inform subsurface nutrient flux monitoring locations at the land-sea interface and guide coastal management measures.</p>