Coastal subtropical Southern American shallow lakes as unique ecosystems for monitoring anthropogenic induced ecosystem changes

The South American Coastal Shallow Subtropical Lakes (SA-CSSL) represent the largest continuous coastal shallow-lake system of its kind globally — a 1,000 km belt of over 100 wind-exposed polymictic lakes and lagoons - mostly freshwater due to high precipitation, groundwater inputs and large catchments — arrayed along southern Brazil into eastern Uruguay. The SA-CSSL lakes formed during the Quaternary as barrier–lagoon systems - lagoons impounded behind coastal sand barriers, a unique and peculiar feature in the context of shallow lakes. Despite their regional and global relevance, subtropical shallow lakes remain under-represented in limnology, making SA-CSSL a critical research target that goes beyond temperate-dominated research. The region spans strong climatic and anthropogenic gradients and is directly influenced by the El Niño Southern Oscillation (ENSO), creating a natural laboratory for comparative and replicated studies on ecosystem processes, biodiversity and resilience. Here, we synthesise the current knowledge on the system’s origin, structure, functioning and pressures and formulate a forward-looking plan for coordinated research and monitoring. Drawing on the strategic outcome from a 2025 workshop in Brazil, we delineate four representative aquatic subsystems with historical monitoring and active projects — the Tramandaí River System, Patos Lagoon System, Mangueira–Mirim System and Uruguayan Lagoon System — as sentinels for integrated observation and research. Key anthropogenic and climatic stressors comprehensively documented include eutrophication, urban and agricultural runoff and emerging contaminants (e.g. pharmaceuticals, pesticides, microplastics), alongside rapid landscape change and more frequently occurring extreme weather events due to climate change. We further outline priority research topics that leverage the system’s scale and gradients: (i) pollutant and “novel entity” surveillance combining analytical chemistry with microbial and molecular biomarkers; (ii) biodiversity and community-assembly studies across ecotones and salinity transitions; (iii) remote-sensing–enabled lake modelling and early-warning indicators; (iv) designs for extreme inflow events; and (v) transboundary governance cases. To align local action with global needs, we align a monitoring framework with planetary boundaries, propose indicators and highlight data-infrastructure needs. We position SA-CSSL as a globally unique large-scale model for subtropical shallow lakes and a collaborative nexus for testing ecological theory and managing freshwater under accelerating climate and societal change.