<p>Environmental and spatial filtering are key drivers of metacommunity assembly in streams. Their relative importance may depend on factors such as network connectivity or species’ dispersal abilities. However, studies comparing different taxonomic groups across connectivity gradients in the same area remain rare. Here, we assessed metacommunity assembly in two groups with contrasting dispersal abilities (diatoms and macroinvertebrates) in a Mediterranean catchment where connectivity is disrupted by stream flow cessation. We combined local predictors (e.g., water and habitat quality) with drying variables at local and regional scales to evaluate the role of environmental and spatial factors using variation partitioning at annual and seasonal scales. Diatoms were mainly shaped by spatial factors, while macroinvertebrates responded more to local environmental conditions. High dispersal in diatoms and ongoing input from suboptimal habitats suggest a mass-effect archetype. In contrast, macroinvertebrates showed dispersal limitation, preventing mass effects but allowing for species-sorting. Drying effects varied seasonally, with a lower influence in spring. Considering flow direction improved the explanation of diatom distributions, shedding light on drift processes. These results underscore the importance of analyzing aquatic communities independently, accounting for taxonomic and seasonal differences, particularly in dynamic systems such as temporary rivers. Multi-taxon studies incorporating seasonal variability and river network connectivity are essential to deepen our understanding of biodiversity and ecosystem functioning. Such approaches can guide conservation and management efforts in temporary rivers worldwide, which are increasingly prevalent owing to global change.</p>