The mandate to maintain at least a good ecological status of all surface waters has led to increased river restoration projects across Europe in the past two decades. The aim is to re-establish the hydromorphological situation and reverse the damage to freshwater ecosystems. In this study, we evaluated the restoration measures in a small stream in the State of Saxony, Germany, using the Transient River Habitat Modelling for Macrozoobenthos (TRiMM). The model was established using the Physical habitat template, covering physical habitat variables (flow, substrate, and thermal regime). It also introduces the application of a fuzzy approach to investigate river physical conditions and their effects on biological indicators like macrozoobenthos. Three taxa, namely Ancyls fluviatilis, Ephemera danica, and Gammarus fossarum, with different habitat preferences, were used to investigate the river’s ecological conditions. The model simulated the natural flow conditions from spring to summer, before and after the restoration was implemented. The research indicated that the restoration of the studied river sections succeeded in providing suitable habitats for target taxa at varied discharge conditions.