In recent decades, tectonic deformation has been reported to be widely distributed throughout the Pampa plain. Northern Pampa plain is a large region generated by aeolian and river megafan sediments accumulated in the distal foreland basin of the Sierras Pampeanas Orientales, over the Quaternary. The extensively partitioned deformation acts as structural controls to runoff and groundwater seepage, generating numerous shallow tectonic lakes. Consequently, two kinds of these lakes typically characterise this region. Regional tectonic depressions are occupied by large lakes that permanently store water and show higher sedimentation rates. The most representative cases are Laguna Mar Chiquita (2000–6000 km2) and Laguna Melincué (103–186 km2). On the other hand, more than one hundred polygonal structural depressions that become waterlogged during extremely wet seasons are present. The first-order structural geomorphological control on the hydrodynamics, the long-term sedimentary record evidencing oscillating climatic conditions, and the long water storage residence observed during extreme events over the last decades promote to categorise and map them as tectonic ephemeral shallow lakes. Geodetic, stratigraphic and geomorphological information suggests that tectonic deformation controlling the development of shallow lakes in pericratonic foreland basins is an active process, rather than a long-term passive control one, as usually proposed.