To develop strategies for the management and protection of aquatic biodiversity in water bodies at the landscape scale, there is a need for information on the spatial organization of diversity in different types of aquatic habitats. In this study, we compared the cladoceran composition and diversity between wheel tracks, pools, ponds, lakes, ditches, and streams, in 18 different areas of Flanders (Belgium). Multivariate analysis revealed significant differences in the composition of cladoceran communities among the different water body types. Average local and total diversity tended to be highest for lakes and lowest for streams. Despite the relatively high number of species supported by lakes, small water bodies seem to contribute considerably more to the total cladoceran richness of an average landscape in Flanders than lakes, because of their high abundance. With respect to biodiversity conservation at the landscape scale, our results point to the importance of maintaining a diversity of water body types of different size, permanence and flow regimes.