After Hurricane Katrina passed through the US Gulf Coast in August 2005, floodwaters covering New Orleans were pumped into Lake Pontchartrain as part of the rehabilitation process in order to make the city habitable again. The long-term consequences of this environmentally critical decision were difficult to assess at the time and were left to observation. In the aftermath of these natural disasters, and in cases of emergency, the proactive use of screening level models may prove to be an important factor in making appropriate decisions to identify cost effective and environmentally friendly mitigation solutions. In this paper, we propose such a model and demonstrate its use through the application of several hypothetical scenarios to examine the likely response of Lake Pontchartrain to the contaminant loading that were possibly in the New Orleans floodwaters. For this purpose, an unsteady-state fugacity model was developed in order to examine the environmental effects of contaminants with different physicochemical characteristics on Lake Pontchartrain. The three representative contaminants selected for this purpose are benzene, atrazine, and polychlorinated biphenyls (PCBs). The proposed approach yields continuous fugacity values for contaminants in the water, air, and sediment compartments of the lake system which are analogous to concentrations. Since contaminant data for the floodwaters are limited, an uncertainty analysis was also performed in this study. The effects of uncertainty in the model parameters were investigated through Monte Carlo analysis. Results indicate that the acceptable recovery of Lake Pontchartrain will require a long period of time. The computed time range for the levels of the three contaminants considered in this study to decrease to maximum contaminant levels (MCLs) is about 1 year to 68 years. The model can be implemented to assess the possible extent of damage inflicted by any storm event on the natural water resources of Southern Louisiana or similar environments elsewhere. Furthermore, the model developed can be used as a useful decision-making tool for planning and remediation in similar emergency situations by examining various potential contamination scenarios and their consequences.