The sustainable management and restoration of streams require tools that capture both spatial and temporal habitat variability and continuity. One such tool is a transient habitat model that can determine spatiotemporal habitat variations. In this study, we applied the transient model to assess how dynamic physical and climatic factors shape habitat availability for the mayfly Ephemera danica in Wiesengrundbach, a partly restored Central European stream. Combining two-dimensional hydrodynamic and morphodynamic simulations with fuzzy logic-based assessments, the model quantifies daily changes in habitat suitability and connectivity. High-resolution field data and two-dimensional modeling reveal how discharge, substrate, and temperature fluctuations interact to structure habitat mosaics. The findings indicate that despite the occurrence of significant seasonal and occasional disruptions, the river maintains a network of stable, suitable habitat patches that support dispersal under the conditions of the simulated dry year. Importantly, declines in habitat suitability occur during peak periods of summer temperatures, suggesting that habitat may be vulnerable if future climate warming increases the frequency and duration of such thermal conditions. By combining spatiotemporal patch dynamics and dispersal analysis, this approach provides insights into resilience and fragmentation of habitats of benthic invertebrates. These results support the need for dynamic species-based modeling to inform conservation and climate adaptation strategies in river systems.