The zooplankton communities of 5 temporary ponds in the Northern part of the Natural Park of the Southwest and Vicentina Coast (PNCSV), Southwestern Portugal, were studied during two consecutive years of contrasting rainfall. A total of ten cladoceran species and eleven copepod species (3 diaptomids, 5 cyclopoids and 3 harpacticoids) were recorded. The community structure varied along the hydrological period of the ponds. Some species were restricted to the early period of the pond (Diaptomus kenitraensis, Hemidiaptomus roubaui, Daphnia hispanica) while others started to build large populations in the middle of the hydroperiod and dominated the communities at the later stages of the hydroperiod: Dussartius baeticus and Ceriodaphnia reticulata dominated the larger ponds, while C. reticulata and Simocephalus exspinosus dominated the smaller ponds. Alpha and beta diversity of cladoceran and copepod species were calculated for the ponds of different hydroperiod length (i.e., water residence time) and area. Alpha diversity was defined as the total diversity of species associated with each pond throughout the annual hydrological period. Copepod and cladoceran communities associated with larger ponds were more diverse than the communities of smaller ponds. As several pond species occur in succession during the length of hydrological period, a longer hydroperiod (2006/2007) allowed for the establishment of a larger number of species than a shorter hydroperiod (2007/2008). Beta diversity was considered as the turnover of species in the gradient of pond area and was higher in the longer hydrological period than in the shorter hydrological period. The degree of diversity change between pairs of ponds was larger between any of the two smaller ponds and any of the larger ponds. This is the first study on the richness of planktonic micro-crustaceans in Portuguese temporary ponds. It is our purpose to increase the knowledge on these taxa to highlight the importance of including this little known, albeit unique, biological diversity when evaluating Mediterranean temporary ponds to conservation purposes.