The Pantanal basin is an old continental margin of the pre-Cretaceous South American Gondwana. The graben of Pantanal itself was formed through the fragmentation of an old Cretaceous shield, in a balancing conjunction with the uplifting of the Andes and of the Brazilian highlands. The topography changed from a basically exorheic pre-Tertiary domed shield, to an endorheic syncline. As the orogenesis progressed, the syncline of the Pantanal sunk deeper and deeper and filled up with alluvional sediments. The Pantanal, as we see it today, represent the history of Pleistocenic climate fluctuations .

The myth of Pantanal as an ancient sea evoked during the 30's the idea of great oil reserves in it. Geologic researches in the area did not demonstrate oil existence or any evidence of sea ingressions in the region. The abundant shells found are fresh water ones and the "saline lagoons" present are in truth bicarbonated waters, without any relation with salt water.