The San Juan sub-basin covers the southern fourth of Chocó Basin and extends from Istmina, in the north to Buenaventura, in the south. The productive cover of the San Juan sub-basin is composed by predominantly marine sediments, deposited during the Cenozoic times, resting on a Cretaceous basement, dominated by oceanic basalts and sediments accumulated in deep-water marine environments. A remarkable feature of the San Juan Sub-basin is the absence of outcrops typical of the Baudó Range, which disappears north of the Rio Docampadó. From a structural point of view, the San Juan sub-basin consists of two regions with different deformation intensity and style (Figure 2):
According to gravimetric maps presented by CARSON (2008), the IDB is associated with a basement high that shows up well in the subsurface west of Middle San Juan Valley. The latter runs southward along the western side of a sedimentary strip whose maximum thicknesses has been estimated to be close to 4500 m, within two small basins located in the southern half of the Middle San Juan River Valley. South of them, in the area of Buenaventura and in the western portion of the San Juan River Delta, the thickness of sedimentary cover increases to over 6000 m.