This paper quantifies sediment contamination by heavy metals in four reservoirs and one lake located downstream from major urban areas in Switzerland. The waterbodies include the Wettingen Reservoir (located on the Limmat River downstream from Zürich), the Klingnau Reservoir (on the lower Aare River), the Wohlen Reservoir (downstream from Berne), the Verbois Reservoir (downstream from Geneva) and Vidy Bay (Lake Geneva, city of Lausanne). For all sediment cores and contaminants, a trend is observed from high contaminant values in the lower part of the cores, decreasing to lower concentrations in the upper part of the cores. However, for each site and each element, specific features are recognized. Applying the criteria of the Swiss ordinance on soil protection, all sediment cores must be classified as contaminated by one or more contaminants and at variable levels. From these data, it is concluded that: reservoirs and lakes located downstream from major urban centres in Switzerland have accumulated significant volumes of contaminated sediments in the past, representing the largest, but not the most intensely, contaminated sites on a national scale; the main environmental risk is remobilization of the contaminants and their return to the food chain, particularly by infiltration into the groundwater; and although the processes of remobilization are identified, the conditions of occurrence and the amplitude of the processes are still poorly known. Different options of reservoir and lake sediment management also are discussed and further research topics defined.