Atmospheric acid deposition leads to surface water acidification and eutrophication; meanwhile, climate warming also influences lake water environment. The response of lake ecosystems to their interactive interaction is one of research hotspots in global environmental changes. Southwest China is one of the regions with the highest acid deposition loading all over the world. However, there is a paucity of information on how aquatic environments respond to acid deposition. This study investigated historical documents and diatom communities in a ²¹⁰Pb-dated sediment core collected from Lake Longtan of the Simian Mountains in Chongqing City, to explore aquatic environmental changes and major underlying driving forces during the past century. The results showed that Achnanthidium minutissimum and Encyonema silesiacum were dominant species in Lake Longtan from 1926 to 1968. Subsequently, Lindavia bodanica increased sharply to a peak and then decreased gradually, concurrent with the increases of Aulacoseira alpigena and Aulacoseira ambigua. Taken together, the dominance of circumneutral and alkaliphilous diatoms with few acidophilic species indicated that water column maintained weakly alkaline in Lake Longtan. One potential explanation is that local bedrock (i.e. purple sand shale) and forest soils have strong ability to buffer against the effects of acid deposition. Although water column in Lake Longtan is slightly alkaline at present, diatom-inferred alkalinity loss and the increase of mesotrophic species after the 1980s indicated that acid deposition had caused a decrease in alkalinity but an increase in nutrient level. Warming-driven thermal stratification and nutrient enrichment probably resulted in a decrease in L. bodanica, a taxon preferring mixing and oligotrophic environment. Recent decreases in meso- and eu-trophic diatoms reflected eutrophication alleviation in Lake Longtan.