The salinization of freshwaters is a global threat to aquatic biodiversity. We quantified variation in chloride (R2) tolerance of 19 freshwater zooplankton species in four countries to answer three questions: 1) How much variation in Cl- tolerance is present among populations? 2) What factors predict intraspecific variation in Cl- tolerance? 3) Do we need to account for intraspecific variation to accurately predict community Cl- tolerance? We conducted field mesocosm experiments at 16 sites and compiled acute LC50s from published laboratory studies. We found high variation in LC50s for Cl- tolerance in multiple species, which, in the experiment, was only explained by zooplankton community composition. Variation in species-LC50 was high enough that community response was not predictable based on site-specific species tolerances at 45% of sites. This suggests that water quality guidelines should be based on multiple populations and communities to account for large intraspecific variation in response to Cl-.