River systems have been the subject of studies that address their ability to transfer water and sediments continuously and efficiently. However, works aimed at understanding the geological controls that promote disconnection and sediment storage in temporary semi-arid rivers are scarce. In the semi-arid Northeast of Brazil, the morphostructural context, in line with crustal mechanics, acts on the transmission of materials along the channels, conditioning the spatial juxtaposition between stretches of rocky and alluvial bottom resulting from the creation of accommodation spaces and sediment storage that promote primary river disconnection. By applying morphometric indices to the Carna & uacute;ba River watershed, state of Rio Grande do Norte, this work identified how the action of crustal deformations, conditioned by the reactivation of shear-zones, and drainage superimposition to lithological units discordantly disposed to the main channel, contributed to creating morphological compartments dominated by aggradation. The data indicate that the Cenozoic tectonics operating in the watershed created accommodation spaces controlled by knickpoints, grabens and rocky sills. These structures functioned as storage basins throughout the Quaternary and engender current scenarios of river disconnection that add to the intermittency characteristics inherent to the fluvial environment of the Brazilian semi-arid region.