Species distribution models (SDMs) are statistical tools to identify potentially suitable habitats for species. For SDMs in river ecosystems, species occurrences and predictor data are often aggregated across subcatchments that serve as modeling units. The level of aggregation (i.e., model resolution) influences the statistical relationships between species occurrences and environmental predictors—a phenomenon known as the modifiable area unit problem (MAUP), making model outputs directly contingent on the model resolution. Here, we test how model performance, predictor importance, and the spatial congruence of species predictions depend on the model resolution (i.e., average subcatchment size) of SDMs. We modeled the potential habitat suitability of 50 native fish species in the upper Danube catchment at 10 different model resolutions. Model resolutions were derived using a 90-m digital-elevation model by using the GRASS-GIS module r.watershed. Here, we decreased the average subcatchment size gradually from 632 to 2 km2. We then ran ensemble SDMs based on five algorithms using topographical, climatic, hydrological, and land-use predictors for each species and resolution. Model evaluation scores were consistently high, as sensitivity and True Skill Statistic values ranged from 86.1–93.2 and 0.61–0.73, respectively. The most contributing predictor changed from topography at coarse, to hydrology at fine resolutions. Climate predictors played an intermediate role for all resolutions, while land use was of little importance. Regarding the predicted habitat suitability, we identified a spatial filtering from coarse to intermediate resolutions. The predicted habitat suitability within a coarse resolution was not ported to all smaller, nested subcatchments, but only to a fraction that held the suitable environmental conditions. Across finer resolutions, the mapped predictions were spatially congruent without such filter effect. We show that freshwater SDM predictions can have consistently high evaluation scores while mapped predictions differ significantly and are highly contingent on the underlying subcatchment size. We encourage building freshwater SDMs across multiple catchment sizes, to assess model variability and uncertainties in model outcomes emerging from the MAUP.