The salinity in a coastal lagoon is a crucial abiotic factor to the species adapted to the brackish water; for example, this is the case for bivalve mussels that have growth and survival rates critically dependent on the salinity. Lagoons with marked river flow seasonality can be periodically flushed to very low salinity levels during the rainy season. In addition, their water exchange with the sea can be very limited, especially for choked lagoons, making the recovery of the salinity levels slow. In this study, models of the salinity dynamics in a choked lagoon for both monthly and intertidal scales were developed. The intertidal model was used to simulate the salinity drop and recovery processes due to runoff events, while the monthly model was coupled with a newly developed heuristic population model for the bivalve mussel Sururu (Mytella falcata ). Thus, the impact of the salinity interannual seasonality on the mussel population was qualitatively investigated. The intertidal model estimated the expected time to be 19 days for the salinity to recover to levels prior to a runoff event with peak flow higher than 500 m3/s. The monthly salinity model satisfactorily represented the interannual seasonality when applied to a historical record including periods of critical salinity levels. The use of the mussel population model indicated that the Sururu stocks during this period were considerably reduced; however, the model results do not indicate the disappearance of this mussel for more than one rainy season. The models developed showed the potential to be used for the management of coastal lagoons and to investigate future scenarios of changes in the lagoon water balance and forecasted sea-level rise. The analytical models presented also showed potential to be used in guidelines for developing and verifying numerical models capable to represent the salinity effects on mussel populations.