The Paranaguá Bay is located on the center-north littoral of the state of Paraná in the south of Brazil. Three natural channels give access to the Atlantic Ocean, denominated as North and Southeast (north of Mel island) and Galheta channel (south of the same island). The last one is the main access to the Paranaguá port, where maintenance dredging activities are necessary for navigation. This study aims to characterize the channel morphological variations from 1972 to 2000. It is our goal also to quantify the sedimentation rates for some critical sections of the channel and to understand the processes of sediment transport along the southern mouth of the bay. The wave front arrives preferentially from southeast, and the alongshore drift of the coastal sediments is toward the northeast. The alongshore sediment flux on the Paranaguá Bay mouth vicinities is characterized by two main fluxes: (1) on the external sector, one contours the terminal lobe of the ebb-tidal delta, deflecting the channel to the northeast. In spite of the rectification attempts, by dredging, channel deflection has persisted through the past decades. (2) On the inner sector, the sediment flux moves up the estuary, along the margin of the Pontal do Sul coastal village, being redirected by the ebb-tide currents proceeding from the Cotinga channel, to the Galheta channel. The tidal currents lose energy on the widest portion of the estuary, and the sediments are deposited there, forming an inner bank. Sedimentation rates calculated for the external sector varied between 19.3 and 229.2 × 10³ m³/mo, but a larger data set is necessary, for the confirmation of this pattern of channel shoaling.