Temporary pools are small and shallow freshwater habitats with a recurring dry phase and intermittent stagnant water. They are particularly well represented in semiarid and karstic regions of the world, where they form during the lentic phase of intermittent rivers and streams. Despite the increasing research interest in such habitats, community ecology studies are still rare, and thus far, have mostly focused on the lotic hydrological phase. Mayflies are among the most abundant benthic macroinvertebrates in freshwater ecosystems, showing high sensitivity to habitat degradation, which makes them widely used in bio-monitoring programs. Mayfly taxonomic and functional diversity, as well as their relationship with environmental variables, were investigated in the temporary pools formed during the lentic phase of three karst intermittent rivers in the Mediterranean. Pools were characterized by river-specific species composition. However, mayfly taxonomic and functional diversity metrics were comparable among the pools of the three rivers. They were influenced by distance from the river’s source and physicochemical water properties, particularly water temperature, conductivity, chemical oxygen demand, and nitrate concentration. Those are related to habitat morphology, substrate composition, and the level of anthropogenic impact. Although the investigated small and shallow temporary pools represent rather harsh habitats, they were inhabited by some species rare in Croatian freshwater habitats (Procloeon pennulatum and Nigrobaetis niger). Our findings suggest that the conservation value of Mediterranean intermittent rivers does not rest upon a single hydrological phase, but upon an interchange of different phases.