Secondary salinisation of rivers and streams is a global and growing threat that might be amplified by climate change. It can have many different causes, like irrigation, mining activity or the use of salts as deicing agents for roads. Freshwater organisms only tolerate certain ranges of water salinity. Therefore secondary salinisation has an impact at the individual, population, community and ecosystem levels, which ultimately leads to a reduction in aquatic biodiversity and compromises the goods and services that rivers and streams provide. Management of secondary salinization should be directed towards integrated catchment strategies (e.g. benefiting from the dilution capacity of the rivers) and identifying threshold salt concentrations to preserve the ecosystem integrity. Future research on the interaction of salinity with other stressors and the impact of salinization on trophic interactions and ecosystem properties is needed and the implications of this issue for human society need to be seriously considered.