The Pampa plain is located in the central part of Argentina. This region shows heterogeneity in its soils and climate, and has been subjected to high anthropic pressure, being dominated by agriculture and cattle breeding. It hosts thousands of permanent shallow lakes that are characterized as polymictic, naturally eutrophic or hypereutrophic, and slightly alkaline. Currently, most of them are in a phytoplankton-turbid regime with a high abundance of phytoplankton. Some lakes remain in a vegetated-clear regime, dominated by submerged macrophytes, and others are in an inorganic-turbid regime with high concentrations of inorganic suspended solids. Factors acting at different scales (local, landscape and regional) interact resulting in the current characteristics of these shallow lakes. We found that the key drivers of phytoplankton chlorophyll a concentration (Chla) in these aquatic systems are total nitrogen (TN) and the percentage of crops in their surrounding area. Management strategies to avoid or diminish the development of anthropic activities—in particular agriculture—in the nearby zones of the lakes should be established to mitigate the deterioration of these shallow lakes.