Abstract The Transbrasiliano Lineament (TBL), a NE-SW trending strike slip system at least 2700 km long, is one of the main structures of the South American Platform. This lineament, along with other structures, influenced greatly the installation and depositional history of the Parana and Parnaiba sedimentary basins. The Agua Bonita Basin (ABB) occurs at an intermediate position between both basins. This work aims to provide information on the origin and evolution of the Agua Bonita Basin, considered a Silurian-Devonian basin, as well as its relationship with the Transbrasiliano Lineament. Geological, aero and ground geophysics data were used to determine a structural geological model for the ABB located in the Brasilia Fold Belt in the Tocantins tectonic province. The airborne geophysical magnetic data used in the study were acquired in the 1970s by the existing 147 ground gravity stations in addition to the 498 new ground gravity and geodetic stations that were added to the existing ones. The analysis of the outcrops allowed identifying the sedimentary facies associations providing new information on the depositional environments. The compilation of existing data, satellite images analysis, geological maps and shaded relief provided an integrated model for the study area. A geological model was proposed for the ABB based on the interpretation, integration, depth analysis and 2D gravity forward modeling according to a theoretical model for an extensional duplex in a strike slip system with flower structures. We observed several segmented gravity anomalies, which were interpreted as steps/faults. This interpretation is consistent with a pull apart basin. According to the depth data estimated by this model, the maximum thickness of the Agua Bonita Formation is 1.6 km and 2.4 km for the precursor rift. The basin has two dextral faults on each border, whose main fault of the TBL strike slip system and the master fault controlling the ABB are observed on the east border of the rift phase. Lineaments perpendicular to the west edge, in addition to those crossing the ABB in the N65E, delineate peculiar magnetic, gravity and geological signatures in the northern part of the basin. The basin is located in the weak region of the TBL and its main eastern fault is dipping sub-vertically to the west. This fault modeled up to the 8 km depth using the gravity data, was also observed in the Tilt Angle of the Total Horizontal Gradient (TAHG) matched filter grid result at approximately 8 km, however this may not be this fault maximum depth. Three main sedimentary-tectonic stages were observed, (i) a Pre-Devonian precursor rift present in the Agua Bonita Basin and Jaibaras Group; (ii) the sag stage developed during the Devonian, when the Paleozoic basins of Parana, Parnaiba and Agua Bonita Basin were connected evidenced by the sedimentary facies and similar thicknesses; and (iii) the Pos-devonian rocks that are probably not preserved in the Agua Bonita Basin.