Floodplain soils along the river Rhine in the Netherlands show a large spatial variability in pollutant concentrations. For an accurate ecological risk characterization of the river floodplains, this heterogeneity has to be included into the ecological risk assessment. In this paper a procedure is presented that incorporates spatial components of exposure into the risk assessment by linking geographical information systems (GIS) with models that estimate exposure for the most sensitive species of a floodplain. The procedure uses readily available site-specific data and is applicable to a wide range of locations and floodplain management scenarios. The procedure is applied to estimate exposure risks to metals for a typical foodweb in the Afferdensche and Deestsche Waarden floodplain along the river Waal, the main branch of the Rhine in the Netherands. Spatial variability of pollutants is quantified by overlaying appropriate topographic and soil maps resulting in the definition of homogeneous pollution units. Next to that, GIS is used to include foraging behavior of the exposed terrestrial organisms. Risk estimates from a probabilistic exposure model were used to construct site-specific risk maps for the floodplain. Based on these maps, recommendations for future management of the floodplain can be made that aim at both ecological rehabilitation and an optimal flood defense.