Land cover maps provide essential input data for various hydromorphological and ecological models, but the effect of land cover classification errors on these models has not been quantified systematically. This paper presents the uncertainty in hydromorphological and ecological model output for a large lowland river depending on the classification accuracy (CA) of a land cover map. Using four different models, we quantified the uncertainty for the three distributaries of the Rhine River in The Netherlands with respect to: (1) hydrodynamics (WAQUA model), (2) annual average suspended sediment deposition (SEDIFLUX model), (3) ecotoxicological hazards of contaminated sediment for a bird of prey, and (4) floodplain importance for desired habitat types and species (BIO-SAFE model). We carried out two Monte Carlo (n ¼ 15) analyses: one at a 69% land cover CA, the other at 95% CA. Subsequently we ran all four models with the 30 realizations as input. The error in the current land cover map gave an uncertainty in design water levels of up to 19 cm. Overbank sediment deposition varied up to 100% in the area bordering the main channel, but when aggregated to the whole study area, the variation in sediment trapping efficiency was negligible. The ecotoxicological hazards, represented by the fraction of Little Owl habitat with potential cadmium exposure levels exceeding a corresponding toxicity threshold of 148 mg d 1, varied between 54 and 60%, aggregated over the distributaries. The 68% confidence interval of floodplain importance for protected and endangered species varied between 10 and 15%. Increasing the classification accuracy to 95% significantly lowered the uncertainty of all models applied. Compared to landscaping measures, the effects due to the uncertainty in the land cover map are of the same order of magnitude. Given high financial costs of these landscaping measures, increasing the classification accuracy of land cover maps is a prerequisite for improving the assessment of the efficiency of landscaping measures.