Giant tsunamis can disturb marine sediments, leading to muddy water in nearshore areas. Marine sediments can be resuspended and transported by tsunamis, as well as by tidal, wind-forced, and density currents in coastal oceans. Marine sediment in coastal oceans around urban areas contains heavy metals and cysts of harmful algae. The resuspension of marine sediments can induce multiple forms of marine pollution, including harmful red tides and heavy metal contamination. This study evaluated heavy metal pollution caused by transport of resuspended sediment with adsorbed zinc in a pilot sea, Osaka Bay, based on a tsunamigenic earthquake scenario along the Nankai Trough, which is predicted to occur within 30 years with approximately 70% probability. Tsunami and three-dimensional ocean simulations were conducted to calculate sediment transport using a particle-tracking simulation based on tsunami-induced sediment resuspension. The simulation results suggest that particles would upwell vertically from the seabed in sediment resuspension areas that would form locally in nearshore regions, and then be transported southward offshore by estuarine circulation. Sediment transported by tidal and wind currents would gradually migrate to the southern offshore region. The remaining sediment carrying zinc in the bay would decrease to less than half of its initial volume over the 20 days following resuspension.