[1] The Southern Brazilian Shelf is a region influenced by freshwater, and the evolution of stratification can present important ecological consequences in this area. The aim of this paper was to investigate the importance of straining and advection processes that affect the stratification and destratification of the water column along the Southern Brazilian inner shelf, a region that is influenced by the Patos Lagoon coastal plume. The study was carried out through 3-D numerical modeling experiments and the results were analyzed using the potential energy anomaly equation and wavelet analysis. Results showed that the potential energy anomaly showed strong variability over a time scale of several days and followed the wind pattern over the study region, and was accompanied by the monthly modulation of river discharge and remote effects associated with variability in oceanic circulation. However, the most important events in synoptic time scales occurred in periods shorter than 20 days and were coincident with the passage of meteorological systems over the study region. Straining and advection were the most important mechanisms for the evolution of stratification in the adjacent coastal region. Nonlinearities and dispersion terms were as important as modulation effects, mainly during periods of high fluvial discharge. Close to the Patos Lagoon mouth, vertical advection explained most of the stratification evolution, due to the morphological characteristics in this region. In the frontal region and far field of the plume, the following two regions must be considered: the northeast part, which is characterized by the convergence of the coastal currents and ebb flows associated with the freshwater discharge that promote the domination of the cross-shore straining and advection, and the southwest part, which is controlled by the coastal currents that result in the domination by alongshore straining and advection and cross-shore advection terms. Close to the mouth of the Patos Lagoon, the occurrence of downward velocities generated downward displacement of the isopycnals, which decreases the potential energy anomalies, and vice versa. Near the frontal region, the anomalies were dependent on the intensity of the fluvial discharge. During moderate to high discharge events, the northeastward currents intensified mixing along shore, which decreased the potential energy anomalies. In the same way, the southwestward currents intensified the spreading of freshwater and increased the stratification and the potential energy anomalies.