The Pampean Plain in Argentina is one of the most extended plain regions of the world with numerous wetland systems and very shallow lakes. Certain anomalies related to geomorphology and shallow lakes’ hydrology are particularly present in a sector of the southern Pampean Plain, specifically, in the southwestern limit of the Quequén Grande River Basin. Here, shallow lakes can be defined as upland-embedded wetlands, characterized by the lack of observable hydrological connectivity due to the absence of surface water flows. The aim of this study was to identify groundwater connectivity of Pampean shallow lakes considered as upland-embedded wetlands and classify them according to their water presence frequency over time and their water source origin based on natural tracers (18O–H2O, 2H–H2O, electrical conductivity and Cl− content). In this work, a methodological framework involving a multitemporal analysis of the Normalized Difference Vegetation Index (NDVI) and the Normalized Difference Water Index (NDWI) derived from Landsat data, in addition to field data is proposed. According to water presence frequency, shallow lakes were classified in four categories: occasionally (89.0 %), regularly (6.7 %), usually (1.9 %) and permanently (2.3 %) with water. Obtained results allowed identifying shallow lakes having low, moderate or high mineralized water due to both different evaporation degree and water sources.