Freshwater ecosystems are becoming saltier due to human activities. The effects of increased salinity can lead to cascading trophic interactions, affecting ecosystem functioning and energy transfer, through changes in community and size structure. These effects can be modulated by other environmental factors, such as nutrients. For example, communities developed under eutrophic conditions could be less sensitive to salinization due to cross-tolerance mechanisms. In this study, we used a mesocosm approach to assess the effects of a salinization gradient on the zooplankton community composition and size structure under eutrophic conditions and the cascading effects on algal communities. Our results showed that zooplankton biomass, size diversity and mean body size decreased with increased chloride concentration induced by salt addition. This change in the zooplankton community did not have cascading effects on phytoplankton. The phytoplankton biomass decreased after the chloride concentration threshold of 500 mg L−1 was reached, most likely due to direct toxic effects on the osmotic regulation and nutrient uptake processes of certain algae rather than as a response to community turnover or top-down control. Our study can help to put in place mitigation strategies for salinization and eutrophication, which often co-occur in freshwater ecosystems.