Seasonal water circulation and residence times in the large (150 km2) and shallow (1.3 m average dry season depth) Nokoué Lagoon (Benin) are analyzed by means of numerical simulations using the three-dimensional SYMPHONIE model. The average circulation during the four primary hydrological periods throughout the year are studied in detail. Despite the lagoon's shallowness, significant disparities between surface and bottom conditions are observed. During the flood season (September-November), substantial river inflow (∼1200 m3/s) leads to nearly barotropic currents (∼7 cm/s), ‘directly’ linking rivers to the Atlantic Ocean. Rapid flushing results in short water residence times ranging from 3 to 16 days, with freshwater inflow and winds driving lagoon dynamics. During the salinization period (December-January) the circulation transforms into an estuarine pattern, characterized by surface water exiting and oceanic water entering the lagoon at the bottom. Average currents (∼2 cm/s) and recirculation cells are relatively weak, resulting in a prolonged residence time of approximately 4 months. Circulation during this time is dominated by tides, the ocean-lagoon salinity gradient, wind, and river discharge (∼100 m3/s). During low-water months (February to June), minimal river inflow and low lagoon water-levels prevail. Predominant southwest winds generate a small-scale circulation (∼3 cm/s) with a complex pattern of multiple recirculation and retention cells. Residence times vary from 1 to 4 months, declining from February to June. During the lagoon's desalination season (July-August), increasing river inflows again establish a direct river-ocean connection, and average residence times reduce to ∼20 days. Notably, a critical river discharge threshold (∼50-100 m3/s) is identified, beyond which the lagoon empties within days. This study highlights how wind-driven circulation between December and June can trap water along with potential pollutants, while river inflows, tides, and the ocean-lagoon salinity gradient facilitate water discharge. Additionally, it explores the differences between residence and flushing times, as well as some of the limitations identified in the simulations used.