The Thirty Years' War (1618-1648) had significant consequences for both human populations and natural ecosystems in Europe. To gain a better understanding of its impact on the local aquatic environment, we analyzed a sediment core from Stadtsee, a lake located in the city of Bad Waldsee, Upper Swabia, using a variety of aquatic biotic and abiotic proxies, including bioindicators, biomarkers, and sedimentological data. Through this multi-proxy approach, we infer changes in aquatic communities and their environment during this tumultuous period. Our findings indicate that this war had a marked impact on the lake ecosystem, as evidenced by changes in diatom assemblages, with declining diatom concentrations and progressively decreasing contributions of hypereutrophic species. These changes suggest a lowering in nutrient supply, possibly due to a reduced load of human and animal waste. This is supported by decreasing productivity (low Si/Ti) and declining δ13Corg values. It appears that the war led to a lake recovery and an improvement in water quality, as suggested by the presence of three bryozoans Plumatella species and the absence of Cristatella mucedo, indicating reduced nutrient levels and a well-oxygenated environment, in agreement with high Mn/Fe ratios. Additionally, the presence of chironomids, such as Corynoneura arctica-type and C. intersectus-type, point to a concomitant decline in temperature. This is consistent with preliminary results obtained by the lipid paleothermometer HDI26. Our study thus highlights the valuable insights provided by bioindicators, biomarkers and sediment geochemistry in a concerted approach about water quality and the health of the Stadtsee ecosystem during the Thirty Years' War.