Changes in climate, flow, and morphology threaten aquatic biodiversity by altering habitat quantity, quality, and distribution, affecting the habitat resources accessible to freshwater species during their life cycles. This results in spatial and temporal discontinuity (e.g., fragmented habitats and long durations of habitat loss). The decrease in habitat connectivity is critical for population persistence, particularly for species with lower mobility like macrozoobenthos. Habitat modeling, used to evaluate environmental changes, generally quantifies habitat suitability but not habitat connectivity, another important factor in species-habitat relationships. This study shows how spatiotemporal habitat variations and species dispersal are used to assess habitat connectivity for benthic species. We use a spatiotemporally explicit approach to estimate patch-scale habitat dynamics due to altered river conditions. The spatial configuration of habitat patches within a river reach influences species colonization. Similarly, the continuous sequence of time during which the patches disappear affects the species’ survival. Dispersal simulation using 2D micro-scale flow field information was carried out to derive spatial connections between habitat patches. Moreover, patch loss duration was considered in the analysis of the connectivity of habitat networks. Our findings showed that fragmented dynamic habitats impacted spatiotemporal connectivity, especially during hydrological extreme events (e.g., rapid augmented flow or prolonged hot summer). Increasing habitat availability may not be enough if species cannot establish themselves due to a loss of spatial or temporal connectivity between patches. The introduced approach can improve knowledge of how spatial arrangements and temporal dynamics affect habitat connectivity across space and time, which may support or optimize habitat management plans.