This report presents past observations and projects the future development of water temperature in Swiss lakes and rivers. Projections are made until the end of the 21st century using the CH2018 climate scenarios. Besides climate change effects on temperature, we also discuss effects on discharge for rivers, and effects on the thermal structure, and specifically the seasonal mixing regime and ice cover of lakes. Observations over the past 40 years show a clear increase in river temperatures, with a mean trend of 0.33 ± 0.03 °C per decade, corresponding to ~80% of the observed air temperature trend. This warming has been continuous over the last four decades and impacts the health of stream ecosystems (e.g. by favouring the spread of fish diseases) and their services (e.g., the water usage for industrial cooling). The temperature rise is more pronounced in the Swiss Plateau than in the Alps, where snow and glacier melt partially mitigates (for now) the effects of increasing air temperature. Conversely, annual average discharge shows no significant trend. Similar trends have also been reported for Swiss lakes with mean summer lake surface temperature increasing by 0.40 ± 0.08 °C per decade since the 1950s. This warming trend affects lake stratification. Warm periods may for instance increase the occurrence of deep-water anoxic conditions, as observed during the 2003 heat wave in Lake Zurich. In mild winters, ice cover duration is reduced in alpine lakes, and winter deep mixing is less intense in large-peri-alpine lakes. The mild winter 2006/7 limited, for instance, the seasonal mixing of Lake Constance to about 60 m depths. Effects of warming on lake thermal structure vary within and between regions, due to both lake and watershed characteristics as well as regional climate change patterns. We simulated the future evolution of stream temperature for 10 catchments in Switzerland for a historical reference period (1990–2000) and two future periods: 2055–2065 (mid-century) and 2080–2090 (end of the century). Results show that the temperature will stabilize by the end of the century for the RCP2.6 scenario (strong CO2 emission reduction), whereas the warming will accelerate with time for the RCP8.5 scenario (business as usual scenario). This expected warming will have significant impacts on the stream ecosystems. Alpine and lowland catchments will experience a similar annual mean temperature increase but display different seasonal effects. While Swiss Plateau rivers will become warmer both in winter and summer (but more in summer), alpine rivers will experience almost no warming in winter but a strong warming exceeding that of air temperature in summer. This is explained by an abrupt decrease in discharge, and by the soil warming resulting from the absence of snow and thus a lower albedo. Lake temperature projections are based on one-dimensional, vertically resolved, hydrodynamic simulations for 29 lakes. The simulated lakes cover a wide range of sizes, depths and water quality, and an altitude range from 200 to 1800 m a.s.l. Simulations indicate substantial changes in lake thermal structure for RCP8.5 with surface temperatures increasing on average by 3.3 °C at the end of the 21st century. This increase is limited to 0.9 °C in the mitigation scenario RCP2.6. We identified an altitude-dependent evolution of the durations of summer and winter stratification as well the ice-covered period. Larger changes in stratification duration are expected to occur at higher altitude lakes. Yet, these lakes will still maintain winter stratification and a shortened icecovered period while lower altitude lakes (below ~1500 m a.s.l.) risk drastic changes in the mixing regime. e.g., a complete loss of the ice cover and winter stratification under the RCP8.5 scenarios. Such changes in the mixing regime may strongly impact lake ecosystems. These low to mid altitude lakes may therefore be considered as the most vulnerable to climate change.