Mediterranean temporary ponds are unique ecosystems characterized by alternating flooding and drying phases, which support highly specialized plant communities. However, these habitats are increasingly threatened by environmental pressures that may alter their ecological functioning. The aim of this study was to evaluate the effects of hydrological conditions and manure on the vegetation of Mediterranean temporary ponds in the Moroccan Middle Atlas. Sediments collected from four temporary ponds were used in a microcosm experiment. Different manure treatments and hydrological regimes (flooded, moist, and dry) were applied to assess their effects on plant density, species richness, and floristic composition. The results showed that manure significantly affected total plant density as well as the density of aquatic, annual aquatic, and perennial aquatic plants, while no significant effect was observed on species richness. In contrast, hydrology had a strong influence on density, species richness, and plant community composition. Floristic composition analyses also revealed significant effects of manure, hydrology, and their interaction. These findings highlight the key role of hydrological conditions in maintaining biodiversity and ecological functioning in Mediterranean temporary ponds, whereas manure mainly influences plant abundance. This study improves our understanding of the ecological processes governing these habitats and provides useful information for their conservation and sustainable management.