The likelihood of an ecological system to undergo undesired regime shifts is expected to increase as climate change effects unfold. To understand how regional climate settings can affect resilience; i.e., the ability of an ecosystem to tolerate disturbances without changing its original structure and processes, we used a synchronized mesocosm experiment (representative of shallow lakes) along a latitudinal gradient. We manipulated nutrient concentrations and water levels in a synchronized mesocosm experiment in different climate zones across Europe involving Sweden, Estonia, Germany, the Czech Republic, Turkey and Greece. We assessed attributes of zooplankton communities that might contribute to resilience under different ecological configurations. We assessed four indicator of relative ecological resilience (cross-scale, within-scale structures, aggregation length and gap size) of zooplankton communities, inferred from discontinuity analysis. Similar resilience attributes were found across experimental treatments and countries, except Greece, which experienced severe drought conditions during the experiment. These conditions apparently led to a lower relative resilience in the Greek mesocosms. Our results indicate that zooplankton community resilience in shallow lakes is marginally affected by water level and the studied nutrient range unless extreme drought occurs. In practice, this means that drought mitigation could be especially challenging in semi-arid countries in the future.