The hydrologic and geochemical conditions that prevail in Mediterranean temporary ponds (MTPs), create a unique environment for many rare and endangered species. Mediterranean temporary ponds are habitats of high ecological value, which are vulnerable to imminent climatic changes, as well as to human activities. This article examines the hydrology and the nitrogen and phosphorous geochemical cycles of four MTPs in Crete. Field and laboratory studies provided the necessary information for the development of a conceptual understanding of the hydrologic and biogeochemical processes that affect the fate of nitrogen and phosphorous in these MTPs. Their hydrology was driven by deposition, infiltration, and evaporation. The hydroperiod of the ponds varied between 40 and 160 d. Mineralization and nutrient release capacity experiments illustrated the significant role that MTP sediments played in enhancing the geochemistry of the aqueous phase. Such ecosystem functions (i.e., mineralization, nutrient release) exhibited high variability among MTPs necessitating site-specific studies with immediate implications to management. It is very important to understand the local hydrogeochemical and climatic conditions to ensure appropriate environmental measures for their management and conservation.