Shallow lakes are distinctive aquatic ecosystems of the Pampean region. In this paper, climatic, morphometric and chemical-environmental aspects of six lacustrine bodies of the Salado River basin, Buenos Aires, are analyzed. The climatic variability of the region was estimated and linked to the behavior of each water body during the studied period (2017–2018); precipitations displayed deviations from the mean values, with periods of deficit in spring and summer, and excess in autumn. The analysis of satellite images showed a group of lakes with very low variation of the morphometric parameters because they have gates that keep the water level constant. On the contrary, those without anthropic intervention displayed a greater morphometric variability, since the water levels have been directly linked to local weather fluctuations. From a chemical-environmental perspective, changes were observed both at the regional (p = 0.015) and local (p = 0.0014) levels. Differences among sites cannot be characterized by a single variable but by a set of them. The dominant cation in the Pampean shallow lakes is the Na+ coming from the contact of groundwater with loessic sediments. Lakes showed a particular anionic dominance that not following a seasonal but a particular pattern. These are mainly linked to the characteristics of the substrate (presence of marine sediments or gypsum deposits). The great vulnerability of these environments to global and regional climatic changes, anthropic modifications and a large number of shallow lakes in the area, allow finding different scenarios (geomorphological, ecological, hydrogeological, etc.) to assess their vulnerability and predict their behavior against future climate scenarios in an economically important area for Argentine.