A field survey of zooplankton communities was carried out in 32 recently established tropical semi-arid reservoirs in the highlands of Northern Ethiopia with the aim to identify to what extent environmental factors determine species composition of the cladoceran community in such isolated and young reservoirs. To address seasonal variation, the survey was carried out both at the beginning and the end of the dry season. A total of 15 species of cladocerans were identified. Daphnia was the most abundant cladoceran genus, and was present in all reservoirs. Using presence–absence data, no association between cladoceran community composition and geographic distance was found. RDA results indicate that the set of environmental variables that explained cladoceran community composition differed among seasons. Depth, altitude and fish biomass showed a significant association with cladoceran community composition during the wet season, whereas variation in cladoceran community structure was associated with phytoplankton biomass in the dry season. The relative abundance of Daphnia was much higher in the pelagic than in the littoral zone of our study systems. Two key groups of pelagic filter-feeding cladocerans, Diaphanosoma and Daphnia, showed a clear pattern, in which one or the other tended to strongly dominate the community. In addition, we observed a negative association between dominance of Daphnia in the zooplankton community and dominance of cyanobacteria in the phytoplankton community.