Lentic ecosystems act as sentinels of climate change, and evidence exists that their sensitivity to warming varies along a latitudinal gradient. We assessed the effects of nutrient and water level variability on zooplankton community composition, taxonomic diversity and size structure in different climate zones by running a standardised controlled 6-months (May to November) experiment in six countries along a European north–south latitudinal temperature gradient. The mesocosms were established with two different depths and nutrient levels. We took monthly zooplankton samples during the study period and pooled a subsample from each sampling to obtain one composite sample per mesocosm. We found a significant effect of temperature on the community composition and size structure of the zooplankton, whereas no effects of water depth or nutrient availability could be traced. The normalised size spectrum became flatter with increasing temperature reflecting higher zooplankton size diversity due to higher abundance of calanoid copepods, but did not differ among depths or nutrient levels. Large-bodied cladocerans such as Daphnia decreased with temperature. Taxonomic diversity was positively related to size diversity, but neither of the two diversity measures demonstrated a clear pattern along the temperature gradient nor with nutrient and water levels. However, genus richness decreased at the warm side of the temperature gradient. Our experiment generally supports recent empirically based findings that a continuing temperature increase may result in lower genus richness and lower abundance of large-sized zooplankton grazers, the latter likely resulting in reduced control of phytoplankton.