The long-term terrestrial and aquatic ecosystem dynamics spanning between approximately 6200 and 4800 cal BP were investigated using pollen, diatoms, pigments, charcoal, and geochemistry from varved sediments collected in a large stratified perialpine lake, Lago Grande di Avigliana, in the Italian Alps. Marked changes were detected in diatom and pigment assemblages and in sediment composition at ~4900 cal BP. Organic matter rapidly increased and diatom assemblages shifted from oligotrophic to oligo-mesotrophic planktonic assemblages suggesting that nutrients increased at that time. Because land cover, erosion, and fire frequency did not change significantly, external nutrient sources were possibly not essential in controlling the lake-ecosystem dynamics. This is also supported by redundancy analysis, which showed that variables explaining significant amounts of variance in the diatom data were not the ones related to changes in the catchment. Instead, the broad coincidence between the phytoplankton dynamics and rising lake-levels, cooler temperatures, and stronger spring winds in the northern Mediterranean borderlands possibly points to the effects of climate change on the nutrient recycling in the lake by means of the control that climate can exert on mixing depth. We hypothesize that the increased P-release rates and higher organic-matter accumulation rates, proceeded by enhanced precipitation of iron sulphides, were possibly caused by deeper and stronger mixing leading to enhanced input of nutrients from the anoxic hypolimnion into the epilimnion. Although we cannot completely rule out the influence of minor land-cover changes due to human activities, it may be hypothesized that climate-induced cumulative effects related to mixing regime and P-recycling from sediments influenced the aquatic-ecosystem dynamics.