Salinization of aquatic systems is predicted to increase due to climate and land use changes. Nevertheless, community responses may be different according to the ecosystem characteristics and contextual scenarios. Small flowing waters are particularly vulnerable to salinization, which may impact on the biodiversity and ecosystem processes, but this remains unclear. We conducted a study in 42 lowland streams characterized by overall high nutrient levels along a salinity gradient between 2 and 160 g L⁻¹ to analyze changes in zooplankton structural and functional metrics, and the grazing effects of zooplankton on phytoplankton affecting the energy transfer. Generalized additive models revealed that the analyzed metrics were relatively influenced by salinity, with factors related to trophic conditions playing an important role as well. Total abundance and biomass decreased along the salinity gradient while increasing at intermediate soluble reactive phosphorous concentrations (SRP) in the former and with a linear increase in the SRP in the latter case. Taxonomic richness decreased with salinity and dissolved inorganic nitrogen, with species replacement toward saline-tolerant ones according to the compositional and optimums analyses. In opposite, functional richness did not display any specific trend within the environmental gradients. This explains why zooplankton compositional changes were not reflected into shifts in the grazing pattern on phytoplankton, which was in turn driven by SRP and dissolved oxygen concentrations. Further research is a critical requirement in these poorly studied ecosystems for planning mitigation actions to the co-occurrence of eutrophication and salinization in a fast changing world.