Climate change is an increasing threat to freshwater ecosystem goods and services. We review recent research regarding the direct and indirect impacts of climate change on freshwater ecosystems and the severity of their undesirable effects on ecosystem processes and services. Appropriate management strategies are needed to mitigate the long-term or irreversible losses of ecosystem services caused by climate change. To address this, this review puts forward a threshold-based management framework as a potential platform for scientists, decision makers and stakeholders of freshwater ecosystems to work together in reducing risks from climate change. In this framework, the susceptibility of local freshwater ecosystems to change beyond thresholds is continuously investigated and updated by scientists, used to design policy targets by decision makers, and used to establish mitigation measures by local stakeholders.