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In many countries water quality is a major concern for drinking water management authorities. Freshwater is a limited resource and the demand for good-quality water from natural aquatic systems is therefore high. Additional stress arises from anthropogenic emissions of nutrients, chemicals, pathogens, heat and hydrological alterations as well as from the ongoing global climate change. In this thesis the relevant recent past, present and future factors affecting water quality in the perialpine Lake Biel, used as a source for drinking water, was investigated. Through measurements in the field combined with hydrodynamic logical modelling in one and three dimensions, optimal locations for forthcoming lake water intakes was identified. Water quality properties considered were temperature, oxygen, suspended sediment concentration (SSC) and the risk of subaqueous mass movements. The results identified the forthcoming changes expected in Lake Biel due to the upcoming decommission of the Mühleberg Nuclear Power Plant (MNPP) in 2019. This plant currently release ~700 MW of heat into the upstream Aare River in the form of cooling water. The removal of this anthropogenic thermal source will decrease future lake temperature by ~0.3 °C (volume average). Due to seasonal river discharge patterns, the main impact of the plant closure will occur during winter. Minor effects are expected in summer in the form of moderately weaker lake stratification. Furthermore, the current fate of thermal pollution emitted from MNPP was linked to the hydraulic residence time of Lake Biel. While short-term anthropogenic thermal impacts in Lake Biel can be large, the system is additionally experiencing continuous warming up to ~0.1 °C per decade (volume average) by the ongoing climate change. The climate effect on Lake Biel and its primary tributary, the Aare River, was investigated as well as compared to the much larger Lake Geneva and Rhône River. Climate change causes seasonal river discharge shifts resulting in enhanced river warming in summer and diminished warming in winter, while at the same time SSC increases in winter and decreases in summer. Differences in temperature as well as warming rates between rivers and lakes in turn resulted in a discharge and hydraulic residence time-dependent decrease in climate warming of lakes. Furthermore, deep-water renewal in both lakes is predicted to increase in summer and decreases in winter, possibly influencing the replenishment of deep water oxygen. Additionally, sedimentation patterns in Lake Biel were examined and linked to the historical diversion of the Aare River into the lake. The majority of sediment supplied to Lake Biel (~80 %) came from large SSC events in the Aare. These events resulted in a selective particle settling pattern, which concentrated sedimentation on the shallow shelf area North-East of the Aare delta. Both the large SSC events as well as this selective sedimentation pattern were connected to weather fronts coming in from the Atlantic Ocean. The research performed here opens up for further promising interdisciplinary research between Meteorology, Climatology, Hydrology and Sedimentology. Inland water management would benefit through increased knowledge regarding the propagation of particles and/or anthropogenic heat, from river catchments into downstream lakes and sediments.