Human-mediated salinity increases are occurring in freshwaters globally, with consequent negative effects on freshwater biodiversity. Salinity comprises multiple anions and cations. While total concentrations are typically used to infer effects, individual ion concentrations and ion ratios are critical in determining effects. Moreover, estimates of toxicity from single-species laboratory tests, may not accurately predict relative effects on populations and communities. Here, we compared salinity increases from synthetic marine salts and sodium bicarbonate in an outdoor mesocosm experiment in southeastern Australia. We found different effects of salt types on stream macroinvertebrates at the population and community levels, where similar effects were predicted from single-species laboratory tests. Our results caution against the use of single-species laboratory-derived toxicological data to predict both environmentally safe salinity levels and the relative effects of different salt sources on freshwater biodiversity.