Viruses are important pathogens in both marine and fresh water environments. There is a strong interest in using bacteriophages as tracers because of their role as model viruses, since dissolved chemical tracers may not adequately describe the behavior of viruses that are suspended colloids. Despite a large number of studies that examined the transport of bacteriophages in the subsurface environment, few studies examined phage transport in large and complex surface water systems. In this paper we report the results of a dual tracer study on a 40 km reach of the Grand River, the longest river in Michigan, and we examine the performance of bacteriophage P22 relative to a chemical tracer (Rhodamine WT). Our analysis based on the transient storage (TS) model indicated that P22 can be successfully used as a tracer in complex surface water environments. Estimated P22 inactivation rates were found to be in the range 0.27−0.57 per day (0.12−0.25 log10 per day). The highest inactivation rate was found in a reach with high suspended solids concentration, relatively low dissolved organic carbon content, and sediment with high clay content. Estimated TS model parameters for both tracers were found to be consistent with surficial geology and land use patterns. Maximum storage zone sizes for the two tracers were found in different river reaches, indicating that different processes contributed to TS within the same reach for the two tracers. This model can be used to examine the arrival times and concentrations of human viral pathogens released from untreated sewage at recreational areas.