This paper outlines a procedure that quantifies the impact of different sources of spatial variability and uncertainty on ecological risk estimates. The procedure is illustrated in a case study that estimates the risks of cadmium for a little owl (Athene noctua vidalli) living in a Dutch river flood plain along the river Rhine. A geographical information system (GIS) was used to quantify spatial variability in contaminant concentrations and habitats. It was combined with an exposure and effect model that uses Monte Carlo simulation to quantify parameter uncertainty. Spatial model uncertainty was assessed by the application of two different spatial interpolation methods (classification and kriging) and foraging ranges. The results of the case study show that parameter uncertainty is the main type of uncertainty influencing the risk estimate, and to a lesser extent spatial variability, while spatial model uncertainty was of minor importance. Compared to the deterministically calculated hazard index for the little owl (0.9), inclusion of spatial variability resulted in a median hazard index that can vary between 0.8 and 1.4. It is concluded that a single estimator for a whole flood plain may over- or underestimate risks for specific parts within the flood plain. Further research that expands the procedure presented in this paper is necessary to improve the incorporation of spatial factors in ecological risk assessment.