Temporary ponds represent ecologically important habitats that support high species diversity and provide essential ecosystem services, particularly in certain countries surrounding the Mediterranean Sea, where natural lakes are scarce. Israel is located along the southeastern Mediterranean coast and features Mediterranean and arid climatic zones that vary in a variety of meteorological parameters. Temporary ponds are prevalent throughout Israel, including the Mediterranean coast, Mediterranean mountain (i.e., Galilee region), and arid climatic zones. These temporal ponds harbor diverse invertebrate communities that exhibit significant spatial and temporal variations. Among these communities, Monogonont rotifers are notably one of the most diverse and abundant groups. Despite their significant role in aquatic food webs, rotifers are often overlooked in environmental studies, likely due to their small size and difficulties associated with their taxonomy. Resilient resting eggs produced by Monogonont rotifers during periods of unsuitable environmental conditions serve as significant source of propagules that drive the recolonization of temporary ponds upon rehydration, thereby influencing the dynamics of the pond community and metacommunity organization. Here, we examined the diversity of Monogonont rotifers by rehydrating sediment from 30 temporary ponds across Israel. Our analysis identified 39 species, with 25 (64%) of them being reported for the first time in Israel. We found the highest diversity of Monogonont rotifers in the Mediterranean coast region, which is characterized by low altitude, long hydroperiod, and relatively low mean summer daily maximum temperature, while the lowest diversity was found in the Arid region which is characterized by high altitude, short hydroperiod, and high mean summer daily maximum temperature. Our findings suggest that altitude, hydroperiod and mean summer daily maximum temperature are important parameters associated with the observed biodiversity patterns. Our metacommunity analysis further revealed a small contribution of geographic distance (2%) and environmental factors (1%) in shaping rotifer metacommunities. We also found a significant positive correlation among community composition, environmental distance (i.e., Gower’s distance) and geographic distance, possibly due to a linearity in the sampling set-up. Overall, our study highlights the importance of temporary ponds as significant habitats for diverse rotifer communities and emphasizes the need to further study “micro” invertebrate diversity in these unique ecosystems.