A two-dimensional circulation and constituent- transport model, SIMSYS2D, was used to simulate tidal-flow, circulation, and flushing characteristics in Charlotte Harbor. The model was calibrated and verified against field observations of stage,discharge, and velocity. Standard errors averaged about 3 percent of the range in stage at the tide stations and between 3 and 10 percent of the range in discharge measured in the inlets for the calibration period. Following calibration and verification, the model was applied to three different conditions. The first condition represented the existing physical configuration and typical freshwater inflow. The second condition represented reduced fresh water inflow, and the third represented an alteration of Sanibel Causeway. All three conditions were evaluated through Lagrangian particle tracks and simulated dye injections. Residual circulation patterns were similar for typical and reduced freshwater inflow, but reduced freshwater inflow increased the residence time in the upper harbor by a factor of two or more. Removal of Sanibel Causeway did not significantly affect residual flows in upper and lower Charlotte Harbor, Matlacha Pass, Gasparilla Sound, or the Gulf of Mexico. Analysis of Lagrangian particle tracks indicated changes in residence times in San Carlos Bay as a result of removing Sanibel Causeway, but the changes were not consistent for all particles. The residence time of 8 particles in San Carlos Bay decreased with removal of the causeway, 1 was unchanged, and the residence time of 3 particles increased. Simulated flushing characteristics of the estuarine system were affected more by reduced freshwater inflow than for typical freshwater inflow. After 30 days of simulation of reduced freshwater inflow, 42 percent of the dye injected into the upper harbor remained in the upper harbor, compared to 28 percent for typical freshwater inflow. The upper harbor has a relatively long flushing time because it is not directly connected to the gulf and some of the dye that exits to the lower harbor returns to the upper harbor by way of a landward residual flow in the deep center channel. The upper harbor is also sensitive to reduced freshwater inflow because it is the subarea closest to freshwater inflow from the Peace and Myakka Rivers. Removal of Sanibel Causeway had a slight effect on the flushing of Pine Island Sound and San Carlos Bay, but had no significant effect in upper and lower Charlotte Harbor.