The Mundaú-Manguaba Estuary Lagoon Complex is located on the coast of Alagoas state in Northeastern Brazil, and consists of two shallow lagoons, Mundaú and Manguaba, that form a system of choked lagoons which are connected to the Atlantic Ocean by a series of narrow channels with a single outlet which dynamically alters its position. This study uses the Hydrodynamic Environmental System, SisBaHiA® to investigate how variations in river discharge and wind influence hydrodynamic circulation, water renewal, salinity and temperature in the lagoons. The free surface positions, obtained by model, were compared with the free surface positions measured at two points of the complex, showing good agreement. The analyses were carried out for dry and wet seasons and extreme events with very high freshwater discharge. The channel system of the lagoons is an efficient filter in reducing tidal variability inside the lagoons. The tidal ranges in the Manguaba and Mundaú Lagoons are 90% and 80% lower, respectively, as compared with the values in the open boundary. The residence time calculated varied between 11 and 365 days and between 2 and 180 days for the Manguaba and Mundaú Lagoons, respectively, making it possible to identify possible stagnation areas. The results from the salt and heat transport model show a prolonged period with low salt concentrations and slow salinity recovery after the rainy season; the water temperature in the lagoons shows little spatial and temporal variation.