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The investigation of the deep structure is a crucial aspect in determining the tectonic evolution and geometry of a basin. To this end, the magnetotelluric (MT) method has been employed to obtain high-resolution two-dimensional electrical resistivity models for the major deep-basement structures of the Pelotas Basin in the passive margin of southern Brazil and Uruguay. The MT resistivity models were generated by applying mathematical inversion to 116 MT sites distributed along three profiles. Specifically, the MT models have identified a conductive layer to depths of 3 km and resistivities ranging from 0 to 80 Ωm, intermediate rocks between the basin/basement, and zones of basement structures with resistivity (< 500 Ωm) and basement rocks with resistivity (> 500 Ωm). The MT data, combined with data from wells, support a tectonic model for the Pelotas Basin that provides more reliable images of the distribution of the main lateral and vertical structures. The resistivity models obtained through the MT method have provided a better understanding of the distribution of the main lateral and vertical structures and the depth of sedimentary cover of the onshore portion of the Pelotas Basin, thus contributing to the development of a more reliable tectonic model for offshore region.