Sediment transport and depositional processes in the Southwest Atlantic Inner Shelf are strongly influenced by the contribution from Río de la Plata and Patos Lagoon fluvial systems. Understanding the behavior of erosive and depositional processes and bed evolution in the region is of utmost importance to address the impacts of anthropogenic activities, climate change and for navigation security. Therefore, this work aims to improve the understanding of such processes, and their temporal and spatial scales of variability. We employed the SISYPHE morphodynamic model coupled with the TELEMAC-3D hydrodynamic model to simulate the resulting depositional and erosional fluxes and the bottom evolution during a period of 8 years (2005–2012). Results indicate that during this period, depositional fluxes mostly exceeded erosional fluxes in the south of the Patos Lagoon mouth, resulting in predominantly positive bottom evolution. On the other hand, erosional fluxes exceeded depositional fluxes to the north of the Patos Lagoon mouth, resulting in predominantly negative bottom evolution. Widespread positive values of bottom evolution are observed along the northern and southern coasts off the Río de la Plata mouth, indicating a general dominance of sediment deposition over erosion. A wavelet analysis showed that fluvial discharge influences the variability of depositional process on an interannual time scale, whereas the synoptic variability is influenced by wind action. Moreover, positive ENSO periods (El Niño) are related to increased depositional fluxes, and decreased depositional fluxes during the negative phase (La Niña), with pronounced effects off Río de la Plata.