In big lakes with strong anthropogenic pressure, it is usually difficult to disentangle the impacts of climate variability from those driven by eutrophication. The present work aimed at the reconstruction of change in the species distribution and density of subfossil Cladocera in Lake Iseo (Italy) in relation to climate and anthropogenic pressure. We related subfossil Cladocera species composition and density in an 80-cm sediment core collected in the pelagic zone of Lake Iseo to long-term temperature trends and phosphorus concentration inferred by diatoms frustules. The Cladocera remains detected in Lake Iseo sediment reflected the species composition and density of modern pelagic Cladocera assemblages. Cladocera rapidly respond to environmental change, and that climate change combined with eutrophication can induce changes in community composition and species density. At the beginning of twentieth century, when global warming was not yet so accentuated, the nutrient increase in water resulted as the principal driver in determining the long-term development of plankton communities and pelagic food web structure. Moreover, catchment-related processes may decisively affect both species composition and density of the lake planktonic communities due to the decrease of lake water transparency induced by input of inorganic material from the catchment area to the lake. The paleolimnological investigation, through the combined study of biotic and abiotic factor, allowed clarifying the synergic effects of the most important drivers of change in lake ecosystems, suggesting that climatic factors should be considered with nutrient availability as determinant element in controlling the temporal development of plankton communities and pelagic food web structure.