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We review the state of the art of limnological studies in Lake Iseo and provide updated data concerning long-term investigations (from 1993 to 2018) carried out on chemical and physical parameters (e.g., oxygen, phosphorus, silicon). Changes observed in Lake Iseo were compared with those reported in other Deep South alpine Lakes (DSLs) to highlight analogies and differences of long-term chemical, physical, and biological patterns. Until the 1960s, Lake Iseo and other DSLs were oligotrophic. The increase of anthropogenic pressure and global warming has led to a progressive and unrecovered process of eutrophication. Moreover, the decrease in frequency of full mixing episodes has induced a state of temporary meromixis. Other changes have been identified over the last two decades, especially concerning the phytoplankton and zooplankton communities, and new emerging chemical pollutants were detected. Given the important ecological and socioeconomic role of Lake Iseo, long-term investigations are of paramount importance to understand the response of the lake ecosystem to climatic and anthropogenic stressors. These two factors can also act coupled with new combined and synergic effects.