[1] The estuarine area of coastal lagoons and freshwater-influenced regions presents periodically stratified and destratified conditions. The Patos Lagoon, one of the most important hydrological resources in South America, is located in the southernmost part of Brazil and exhibits such variable conditions. Therefore the aim of this study was to investigate the contributions of straining and advection to the modulation of stratification conditions in the Patos Lagoon estuarine region using potential energy anomaly budgets. This study was based a three-dimensional hydrodynamic numerical model that provided information for the potential energy anomaly equation and wavelet analysis. Results from the potential energy anomaly time series revealed strong variability over a timescale of several days following local wind action and the river discharge pattern. Each part of the estuary exhibited contrasting regimes that were spatially distributed with a different balance of terms. The upper part was dominated by along-shore currents associated with east-west wind component and gravitational flux. Contribution from cross-shore advection became important in the middle part of the estuary, where there was an increase in superficial area observed. The lower region was controlled by the north-south wind component being influenced by advection, cross-shore straining, and transversal circulation, suggesting that current velocity maintained transversal pressure gradients and further circulation. Nonlinear interactions between deviations in the dispersion terms and vertical density and velocity were important everywhere but were associated with modulation effects.