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Here, we review the state-of-the-art of limnological investigations in the large and deep lakes south of the Alps (DSLs), lakes Garda, Maggiore, Como, Iseo and Lugano. In the pre-industrial age, these lakes were ultra- or oligotrophic. Increasing anthropogenic pressure and the impact of global warming has led to an acceleration of eutrophication and a decrease in the frequency of full mixing episodes, which have induced a state of meromixis in lakes Lugano and Iseo. In the last two decades, other changes have been identified, including fundamental variations in the long-term dynamics and structure of phytoplankton communities, identification of new toxigenic cyanobacteria and cyanotoxins, increases in the introduction and establishment of allochthonous species, and continuous detection of new, emerging chemical pollutants. Overall, these fundamental changes are quickly transforming the features of the DSLs. The ability to document and reconstruct changes in lake aquatic biota and micropollutants was strongly dependent on both research efforts and the availability of technologies to appraise these changes. In this context, the ongoing adoption of new technological tools, such as high-frequency monitoring and high throughput sequencing, is opening the way to a new level of comprehension of physical, chemical and biological processes, and aquatic biodiversity. New outlooks and new conceptual frameworks are necessary to cope with the huge dimensions of high-throughput data and analysis of big data.