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We sought to identify environmental factors influencing crustacean zooplankton species richness in brackish lagoons and to elucidate whether crustacean zooplankton species richness and trophic structure of brackish lagoons differ among two regions with contrasting temperatures. We sampled 35 and 42 brackish lagoons (salinity ranging from 0.3 to 55‰) in Mediterranean Catalonia (NE Spain) and northern-temperate Denmark, respectively. No significant differences were found in total crustacean zooplankton species richness or cladoceran richness between the climatic regions. Calanoid richness was higher in Denmark than in Catalonia, while cyclopoid richness was higher in Catalonia. Salinity was the most important variable associated with zooplankton species richness in both regions, richness of total zooplankton species, cladocerans and cyclopoids being negatively related with salinity. In both regions, a shift occurred from dominance of large filter feeding cladoceran species at low salinities to copepods and small cladoceran species at higher salinities. Cladoceran richness increased with increasing total phosphorus, but was not influenced by total nitrogen or chlorophyll-a. Trophic structure in Mediterranean brackish lagoons showed a more pronounced seasonal variation than in north temperate brackish lagoons. Our results imply that the indirect effects of climate warming, such as changes in salinity and hydrology, will have a larger impact on brackish lagoon ecosystems than the increase in temperature per se. [ABSTRACT FROM AUTHOR]