Growth and development over the past one hundred years has resulted in the construction of causeways and navigational channels in Tampa Bay. Urbanization has lead to bathymetric alterations of the bay, and thus has effectively changed the residual salinity, flow fields, and transport time in Tampa Bay. In this study a numerical ocean model of Tampa Bay was first used to simulate the circulation for 2001-2003 using present day bathymetry. Then, an identical simulation was performed using the bathymetry generated from 1879 depth soundings. The residual (30-day time average) circulation fields and salinity, along with transport times was intercompared for different freshwater inflow conditions to investigate the impacts of these physical alteration. The salinity for the "present" simulation is about 3 psu higher than the "1879" simulation in the areas of upper Middle Tampa Bay, Lower Hillsborough Bay and Old Tampa Bay, a result of a stronger axial pressure gradient associated with the deeper more extensive channels. Velocities are up to 10 cm/s higher in the "present" run than in the "1879" simulation in the areas where water must converge and diverge through the narrow openings of the bridges/causeways. Transport time is short (~10 days) during strong residual circulation, and long (~90 days) during weak residual circulation. Bridges and causeways are associated with longer transport times (~90 days), except in the area North of the Courtney Campbell Causeway. The navigational channel is associated with long transport times during dry periods and short transport time during wet periods.