A 1-D tidal, salinity and water quality model that analyzes the general effects freshwater diversions have on the water quality of the Pontchartrain Estuary over a 17-year period is presented here. Using the modeled live algae concentrations in conjunction with the algal bloom probability model results produces an accurate prediction of algal bloom occurrences between 1990 and 2006. The model predicts that the addition of freshwater diversions into Maurepas swamp and increases to flow in the Bonnet Carré Spillway may cause more intense and frequent algal blooms to occur around the Pontchartrain Estuary. The model also predicts that high nutrient input events that occur earlier in the year (January/February) will not likely have algal blooms associated with them. When nutrient input events (even small events) occur in the late spring or early summer, algal blooms have a high probability of occurring when the salinity, temperature and light levels are sufficient.