Patos Lagoon is a very dynamic environment presenting hydrodynamic fluctuations from synoptic to decadal timescales. Thus, understanding the processes that determine the long term variability is fundamental for the correct coastal planning and management of this region. The main objective of this study is to understand how the freshwater discharge of the main tributaries controls the estuarine hydrodynamics of the Patos Lagoon, when considering long term timescales. Two numerical simulations were carried out using the TELEMAC3D numerical model, the former using freshwater discharge from 1940 to 1973 year (simulation A), and the second simulation using data between 1974 and 2006 year (simulation B). These two periods were selected because before (after) 1973 year, the annual mean freshwater discharge was lower (higher) than the mean value for the whole period (1080 m³/s). The navigational channel discharge, water level, salinity and current velocity differences between both simulations were analyzed. Ebb conditions prevailed over flood conditions for both simulations, but simulation B presented a higher volume of freshwater exported through the coastal zone. Water level differences demonstrated higher values (0.08 meters) close to the Guaiba River, which is the main tributary of the study region, and lower values were observed near to the Patos Lagoon mouth (0 meters). The most significant differences in the mean bottom and surface salinity were observed in the central zone of the estuary and at the Barra Breakwaters. Simulation A presented higher saline intrusion due to lower freshwater discharge, while simulation B showed an increase in the coastal plume intensity, caused by the higher freshwater discharge. The hydrodynamical simulations demonstrated with precision that the freshwater discharge intensity determine the vertical stratification of the estuary.