Levee failure and overtopping as a result of Hurricane Katrina caused major flooding of New Orleans, Louisiana. Floodwaters, which were contaminated with heavy metals, organic chemicals, and fecal coliform bacteria (FCB), were pumped into neighboring Lake Pontchartrain during dewatering. The impact of levee failure on water and benthic sediment concentrations in the lake was investigated by applying a numerical water quality model coupled to a three-dimensional, numerical hydrodynamic model. The model was used to compute water and benthic sediment concentrations throughout the lake for lead, arsenic, benzo(a)pyrene (BaP), and 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE), and water concentrations for FCB. Computed concentrations resulting from actual pumped discharges with levee failure and overtopping were compared to computed concentrations resulting from pumped discharges without levee failure or overtopping, and concentrations from both sets of conditions were compared to ecological water and sediment quality screening guideline values. The model indicated that incremental increases above pre-Katrina benthic sediment concentrations are about a factor of 10 greater with dewatering of the floodwaters than with dewatering of storm water without flooding. However, these increases for the metals are small relative to pre-Katrina concentrations. The results showed that the ecological screening-level sediment quality guideline values were exceeded for BaP and DDE in areas near the south shoreline of the lake as a result of floodwater pump-out, whereas, this was not the case for storm water removal without flooding. The model showed that lake water column concentrations should be about the same during both dewatering conditions regardless of whether there is flooding or not.