We studied the zooplankton community structure in a set of 33 interconnected shallow ponds that are restricted to a relatively small area (‘De Maten’, Genk, Belgium, 200 ha). As the ponds share the same water source, geology and history, and as the ponds are interconnected (reducing chance effects of dispersal with colonisation), differences in zooplankton community structure can be attributed to local biotic and abiotic interactions. We studied zooplankton community, biotic (phytoplankton, macrophyte cover, fish densities, macroinvertebrate densities), abiotic (turbidity, nutrient concentrations, pH, conductivity, iron concentration) and morphometric (depth, area, perimeter) characteristics of the different ponds. Our results indicate that the ponds differ substantially in their zooplankton community structure, and that these differences are strongly related to differences in trophic structure and biotic interactions, in concordance with the theory of alternative equilibria. Ponds in the clear-water state are characterised by large Daphnia species and species associated with the littoral zone, low chlorophyll-a concentrations, low fish densities and high macroinvertebrate densities. Ponds in the turbid-water state are characterised by high abundances of rotifers, cyclopoid copepods and the opposite environmental conditions. Some ponds show an intermediate pattern, with a dominance of small Daphnia species. Our results show that interconnected ponds may differ strongly in zooplankton community composition, and that these differences are related to differences in predation intensity (top-down) and habitat diversity (macrophyte cover).