This study presents data-driven, numerical simulations of 100- and 500-year flood events in the Mississippi River at its intersection with Highway I-694. The study does so by coupling coherent-structure resolving hydrodynamics with bed morphodynamics under live-bed conditions. The study area was about 1.7 miles long, 220 yards wide, and a reach of the Upper Mississippi River near Minneapolis, MN, which contains several natural islands and man-made hydraulic structures. The study employed the large-eddy simulation (LES) and bed-morphodynamic modules of the Virtual Flow Simulator (VFS-Rivers) model--a recently developed, in-house code--to investigate the flow and bed evolution of the river along the reach and near the bridge piers BR 27801 and BR 932. The study integrated data from airborne Light Detection and Ranging (LiDAR), sub-aqueous sonar apparatus onboard a boat, and total station survey to construct a digital elevation model of the river bathymetry and surrounding flood plain. This included islands and bridge piers. A field campaign under base-flow condition was also carried out to collect mean flow measurements via Acoustic Doppler Current Profiler (ADCP) to validate the hydrodynamic module of the VFS-Rivers model. The simulation results for the bed evolution of the river under the 100- and 500-year flood revealed complex sediment transport dynamics near the bridge piers consisting of both scour and refilling events due to the continuous passage of sand dunes. A brief description of the findings in terms of maximum scour depth around individual bridge piers can be found in the executive summary of the report.