Significance The salinity of freshwater ecosystems is increasing worldwide. Given that most freshwater organisms have no recent evolutionary history with high salinity, we expect them to have a low tolerance to elevated salinity caused by road deicing salts, agricultural practices, mining operations, and climate change. Leveraging the results from a network of experiments conducted across North America and Europe, we showed that salt pollution triggers a massive loss of important zooplankton taxa, which led to increased phytoplankton biomass at many study sites. We conclude that current water quality guidelines established by governments in North America and Europe do not adequately protect lake food webs, indicating an immediate need to establish guidelines where they do not exist and to reassess existing guidelines.