Mediterranean endorheic wetlands are strongly affected by local meteorological events, so they undergo frequent unpredictable disturbances, such as episodes of high salinity or desiccation. In this context, salinity and temperature may be crucial for determining the structure of zooplankton communities and regional biodiversity, since they may trigger the hatching of egg bank in different ways. The goal of this study is to assess the combined role of these two variables on the zooplankton assemblage emerging from the egg bank. We hypothesize that temperature and salinity affect the community structure in a non-linear way, that is, both factors interact and modify the magnitude of their effects. We performed a laboratory factorial design where the same sediment was incubated under different thermal and salinity conditions, reducing the potential effects of other possible confusion factors. Community structure was described by measuring cumulative abundances, species composition, richness, and diversity. Our results showed that the community structure was strongly determined by salinity at all experimental temperatures. In contrast, the magnitude of the temperature effect depended on salinity. The high variability among replicates when salinity and temperature increased suggests that climate change might lead to unpredictable patterns of the community emerging from the egg bank.