Models of the fate and transport of river plumes and the bacteria they carry into lakes are developed. They are needed to enable informed decisions about beach closures to avoid economic losses, and to help design water intakes and operate combined sewer overflow schemes to obviate exposure of the public to potential pathogens. This study advances our understanding of river plumes dynamics in coastal waters by means of field studies and numerical techniques. Extensive field measurements were carried out in the swimming seasons of 2006 and 2007 on the Grand River plume as it enters Lake Michigan. They included simultaneous aerial photography, measurements of lake physical properties, the addition of artificial tracers to track the plume, and bacterial sampling. Our observed results show more flow classes than included in previous studies (e.g. CORMIX). Onshore wind can have a significant effect on the plume and whether it impacts the shoreline. A new classification scheme based on the relative magnitude of plume-crossflow length scale and Richardson number based on the wind speed is devised. Previous studies on lateral spreading are complemented with a new relationship in the near field. The plume thickness decreased rapidly with distance from the river mouth and a new non-dimensional relationship to predict thickness is developed. Empirical near field models for surface buoyant plumes are reviewed and a near field trajectory and dilution model for large aspect ratio surface discharge channels is devised. Bacterial reductions due to dilution were generally small (less than 10:1) up to 4.5 km from the river mouth. E. coli decay rates were significantly affected by solar radiation and ranged from 0.2 to 2.2 day-1 which were within the range of previous studies in Lake Michigan. Total coliform survived longer than E. coli suggesting different die-off mechanisms. Mathematical models of the bacterial transport are developed that employ a nested modeling scheme to represent the 3D hydrodynamic processes of surface river discharges in the Great Lakes. A particle tracking model is used that provides the capability to track a decaying tracer and better quantify mixing due to turbulent diffusion. Particle tracking models have considerable advantages over gradient diffusion models in simulating bacterial behavior nearshore that results in an improved representation of bacteria diffusion, decay and transport. Due to the complexity and wide variation of the time and length scale of the hydrodynamic and turbulent processes in the near field (where plume mixing is dominated by initial momentum and buoyancy) and far field (where plume mixing is dominated by ambient turbulence), a coupling technique is adapted. The far field random walk particle tracking model incorporates the empirical near field model. It simulates the transport, diffusion and decay of bacteria as discrete particles and employs the near field output as the source and transports the particles based on ambient currents predicted by the 3D hydrodynamic model. The coupled model improves dilution predictions in the near field. The new techniques advance our knowledge of the nearshore fate and transport of bacteria in the Great Lakes and can be ultimately applied to the NOAA Great Lakes Coastal Forecasting System to provide a reliable prediction tool for bacterial transport in recreational waters.