Invertebrate aquatic assemblages in ponds from Mediterranean wetlands are composed of organisms belonging to different taxonomic groups, which present a wide range of sizes (from small rotifers to large crustaceans or insects). Although they are often sampled and analyzed separately, the ecological links among these organisms should be considered, especially in very shallow waters. In our study, invertebrate assemblages (including micro-, macrozooplankton and macroinvertebrates) were characterized in eight shallow lakes from Mediterranean wetlands in Southeastern Spain. A great spatial and temporal variability in the assemblages and in some environmental features was observed. The community was dominated in abundance and species richness by rotifers in most of the water bodies. Fish greatly contributed to the differences in community composition, as fishless ponds presented abundant and diverse cladoceran populations. Nutrient and chlorophyll-a concentration, conductivity and macrophyte cover had also a great influence on these assemblages, especially in micro- and macrozooplankton. The temporal changes observed in some of these variables affect the proportion of invertebrate biomass of the different groups along the study period. All this environmental heterogeneity produces similar responses in the invertebrate groups, in general well adapted to salinity changes or high trophic conditions. Although the heterogeneity and human disturbances can increase regional diversity, they can cause the disappearance of valuable habitats, and finally, the homogeneity in invertebrate assemblages.