According to the Intergovernmental Panel on Climate Change report released in September 2014, unprecedented changes in temperature and precipitation patterns have been recorded globally in recent decades and further change is predicted to occur in the near future, mainly as the result of human activity. In particular, projections show that the Mediterranean climate zone will be markedly affected with significant implications for lake water levels and salinity. This may be exacerbated by increased demands for irrigation water. Based on long-term data from seven lakes and reservoirs covering a geographical gradient of 52A degrees of latitudes and a literature review, we discuss how changes in water level and salinity related to climate change and water abstraction affect the ecosystem structure, function, biodiversity and ecological state of lakes and reservoirs. We discuss mitigation measures to counteract the negative effects on ecological status that are likely to result from changes in climate and water abstraction practices. Finally, we highlight research required to improve knowledge of the impacts of anthropogenically induced changes on lake water level and consequent changes in salinity.