Assessing zooplankton biodiversity is essential to support freshwater management/conservation programs. Here, we investigated the zooplankton community structure from 180 shallow lakes in northeastern Brazil and analyzed them according to biome (Atlantic Forest or Caatinga), the origin of ecosystems (natural or man-made lakes), and habitat type (pelagic or littoral). Additionally, we provided an updated list of zooplankton species. We registered 227 species (137 Rotifera, 65 Cladocera, 25 Copepoda). The most common species of each major group among all lakes were the cladoceranCeriodaphina cornuta, the rotifersBrachionus havanaensisandLecane bulla, and the copepodTermocyclops decipiens. Species related to aquatic vegetation, as the Lecanidae rotifers and phytophilous cladocerans, were more frequent along Atlantic Forest biome and natural lakes. On the other hand, species that are bioindicators of eutrophic waters were more common at the Caatinga biome and man-made lakes. Atlantic Forest and Caatinga biomes had similar species richness, but different community compositions for all zooplankton groups, reinforcing the Caatinga significance for the Brazilian aquatic biodiversity. The type of habitat was the most important factor structuring species richness, with higher richness in the littoral region when compared to the pelagic. A result of many unique species of Cladocera and Rotifera associated with the aquatic vegetation were observed. The findings demonstrated that conservation/management plans cannot generalize zooplankton species distribution across different biomes, origins and even within a single lake, between the pelagic and littoral zones.