Effect of freshwater discharge on the long-term salt balance in the Northern and Central Indian River Lagoon (IRL) is successfully simulated by a new analytical solution to a water balance-based one-dimensional salt conservation equation. Sensitivity tests show that the salinity levels drop abruptly even during the dry season (November to May) due to the high surface runoff discharge caused by tropical storms, depressions, and passage of cold fronts. Increasing surface runoff and direct precipitation has risen by ten times, lowering the salinity level down to 12psu in the Northern Central zone, and to 17 psu in the Northern zone. However, the salinity level in the Southern Central zone has decreased to 25 psu. High sensitivity of the Northern Central zone to freshwater discharge can be partially explained by a rapid urbanization in this zone. During the dry season, less sensitivity of the Southern Central zone to the increased surface runoff is attributed to the proximity of the zone to the Sebastian Inlet and a strong diffusion condition possibly resulting from the seawater intrusion to the surficial aquifer at the Vero Beach. During the wet season, however, the whole study area is highly sensitive to freshwater discharge due to the weak diffusion conditions. High sensitivity of the IRL to the given diffusion conditions guarantees that the fresh-water release occurs during strong wind conditions, achieving both flood control in the drainage basin and a proper salinity regime in the IRL.