The Atacama Desert is a unique landscape to understand the evolution of the Earth in extremely arid environments. Clay pans are crucial to comprehend the surface and subsurface processes in areas limited by water availability. We present an integrated geoscientific study to investigate the sedimentary deposits of the Paranal clay pan located in the hyperarid core of the Atacama Desert. We used the loop source transient electromagnetic (TEM) method complemented by magnetics and active seismics to resolve different subsurface properties at different spatial scales. A total of 116 soundings were processed, analyzed, and inverted to investigate the resistivity distribution of the clay pan. The TEM-1D inversion results reveal a three-layered resistivity structure with reliable information down to a depth of 250 m. Colluvial and lacustrine sediments reach a maximum thickness of about 160 +/- 10 m. The shape of the lacustrine sediments suggests the presence of an old paleochannel that might be part of the former main Paranal drainage network. In addition, the basement below the clay pan can be partly interpreted as a damaged zone of an inferred strike-slip fault system. Subsequent 2D magnetic modeling confirms the basement depth derived from the TEM results. The seismic transects reveal accurate structural information of the upper 60 m and are consistent with TEM-1D models. High P wave velocities correlate with high electrical conductivity layers and are interpreted as lacustrine sediments. Our work provides key information with respect to the sedimentary thickness above the basement contributing to paleoclimate research in northern Chile.