We reconstructed the changes in the planktonic food web of an oligotrophic subalpine lake over the past century, combining paleoecological methods and historical monitoring data. Analyses of organic matter δ15N from sediment cores show that nutrient enrichment started in the 1910s and intensified from the 1930s. Subsequent changes in sediment organic carbon content and accumulation rates, carotenoid pigment concentrations, organic matter δ13C, and cladoceran subfossil remains show that excess nutrient inputs triggered bottom-up-driven increases in lake primary production, as well as in Daphnia abundance. Daphnia size, however, started to decrease in the late 1930s, indicating an increasing size-selective predation from zooplanktivorous whitefish populations (Coregonus lavaretus) that had been fostered by stocking and increased food availability. Whitefish predation is likely to have indirectly facilitated the establishment of Bosmina longirostris. With decreasing nutrient concentrations, Daphnia abundance decreased, but their size declined, presumably due to an ongoing size-selective predation. At this same time, Bosmina abundance doubled as a likely result of released interspecific competition from smaller Daphnia. δ15N analyses on subfossil cladoceran remains revealed that these changes in cladoceran community structure were accompanied by major changes in the food web. In spite of successful measures to reduce nutrient inputs from the late 1960s and reduced primary production, anoxia still occurs every summer at the lake bottom. These patterns are the consequence of a still relatively high export of phytoplankton-derived organic matter to the sediment as a result of strong top-down effects on the planktonic food chain.