Sediment and plant-associated macroinvertebrates were sampled in six shallow water bodies along the central part of the coast of Mediterranean Spain. The size of ponds, salinity and hydroperiod were highly variable. Seventy-one taxa were recorded, some of them were endemic or uncommon species, evidencing the important contribution of these ponds to biodiversity. Crustaceans and gastropods of biogeographical interest were found in the most primeval site. Correspondence analysis showed that macroinvertebrate assemblages responded to environmental variables such as salinity, temporality and eutrophication. The brackish water fauna was dominated by crustaceans, while oligochaeta and insect larvae were abundant in freshwater conditions. Oligochaetes were abundant at localities with high trophic level, whereas localities with semi-permanent waters were dominated by chironomids. The density of macroinvertebrates was clearly related with trophic state but we did not find significant relationships between density and salinity or water permanence. For plant associated samples our results showed negative relationships between species richness and temporality or salinity, contrary to sediment samples, where the Oligochaeta/Chironomidae ratio in sediments and the percentage of sensitive taxa (Ephemeroptera, Odonata, Trichoptera) were useful indices, and were dependent on pond typology. This study emphasizes the broad ecological variety of ponds found in these wetlands and their importance for biodiversity. Some ponds act as permanent biodiversity reservoirs in fluctuant marshes with seasonal dryness, calling for more attention on their ecological relevance for management strategies.