Sedimentary diatom assemblages from three lakes in the southeastern Swiss Alps were analysed at high temporal resolution since AD 1800. Altered land-use patterns, increasing population and exploitation through tourism are clearly reflected in annually laminated sediments of Lej da San Murezzan (Lake St Moritz) and Lej da Silvaplauna (Lake Silvaplana). Diatom assemblages originally dominated by Cyclotella taxa are replaced by taxa indicating higher total phosphorus (TP) concentrations, such as Asterionella formosa, Fragilaria crotonensis and Stephanodiscus parvus. In Lej da la Tscheppa, located well above the treeline in a catchment that was hardly exposed to human impact, Cyclotella comensis prevails throughout the entire sediment sequence. Quantitative estimates of past TP concentrations were inferred using a newly developed regional diatom-TP inference model based on 119 modern samples. In Lej da la Tscheppa diatoms imply stable, low TP concentrations (~10 µg/l), which can be considered as natural background concentration. Elevated TP levels are inferred for Lej da San Murezzan (max. 60 µg/l) since AD 1910 and for Lej da Silvaplauna (max. 40 µg/l) since AD 1950, corroborated by changes in sedimentary biogenic silica concentration and organic carbon content. Since ~AD 1970 improved waste water management led to a considerable reduction in TP loading in Lej da Silvaplauna and Lej da San Murezzan.