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Abstract Aim Urbanization leads to rapid changes in ecosystem structure and function. Wetlands on university campuses under urbanization pressure could be used as case studies of multidisciplinary aquatic research and good environmental practices promoting sustainability. Methods A paleolimnological study was undertaken in a semi-artificial lake on a university campus in southern Brazil to trace historical impacts and ecological changes back to the mid-1970s through complementary approaches: historical data, nutrients, δ13C and δ15N stable isotopes, diatoms, microplastics and associated microbial community analysis. Results The eutrophication process started to intensify after the lake was used for nocturnal roosting by waterbirds, and especially after the establishment of constructions along the margins with septic tank sanitary sewage, which eventually spilled and leached into the lake. Over decades, we identified a limnological hypertrophication process leading to recurrent cyanobacterial blooms and massive macrophyte proliferation coupled with changes in isotopic ratios and algal occupation with several transitions between shallow lake alternative states. Such a limnological process has resembled the paleolimnological eutrophication trends and isotopic changes in sedimentary organic matter. The microplastic deposition was detected as a proxy for the intensification of urbanization, especially during the construction of the University facilities. Conclusions The combined use of paleolimnological and historical limnological data represents a powerful approach for inferring both natural and cultural impacts on the lake, and identifying management strategies based on such scientific information.