Highly complex interactions between the hydrosphere and biosphere, as well as multifactorial relationships, characterize the interconnecting role of streams and rivers between different elements of a landscape. Applying species distribution models (SDMs) in these ecosystems requires special attention because rivers are linear systems and their abiotic and biotic conditions are structured in a linear fashion with significant influences from upstream/downstream or lateral influences from adjacent areas. Our aim was to develop a modelling framework for benthic invertebrates in riverine ecosystems and to test our approach in a data‐rich study catchment. We present a case study of a 9‐km section of the lowland Kielstau River located in northern Germany. We linked hydrological, hydraulic and species distribution models to predict the habitat suitability for the bivalve Sphaerium corneum in a riverine system. The results generated by the hydrological model served as inputs into the hydraulic model, which was used to simulate the resulting water levels, velocities and sediment discharge within the stream channel. The ensemble model obtained good evaluation scores (area under the receiver operating characteristic curve 0.96; kappa 0.86; true skill statistic 0.95; sensitivity 86.14; specificity 85.75). Mean values for variables at the sampling sites were not significantly different from the values at the predicted distribution (Mann–Whitney U‐test P > 0.05). High occurrence probabilities were predicted in the downstream half of the 9‐km section of the Kielstau. The most important variable for the model was sediment discharge (contributing 40%), followed by water depth (30%), flow velocity (19%) and stream power (11%). The hydrological and hydraulic models are able to produce predictors, acting at different spatial scales, which are known to influence riverine organisms; which, in turn, are used by the SDMs as input. Our case study yielded good results, which corresponded well with ecological knowledge about our study organism. Although this method is feasible for making projections of habitat suitability on a local scale (a reach in a small catchment), we discuss remaining challenges for future modelling approaches and large‐scale applications.