This chapter introduces basic concepts, properties, and principles of different processes in inland surface water and analytical methodologies. The fundamentals of surface water hydrodynamics, including water properties, hydrodynamic processes, Cartesian coordinatebased governing equations, and boundary and initial conditions were reviewed. The fate and transport of contaminants in surface water were introduced. Based on aforementioned theory and principles, two hydrodynamic-water quality models were developed for studying a lake and a river, respectively. A stratified 3D model was used to investigate the circulation and E. coli transport in the nearshore region of Lake Michigan. The modeling results show that stratified phenomenon exists in the near region, and a 3D model is necessary even though a previous 2D model works well for the shallow water environment. A 2D depth-averaged water quality model was developed to estimate the fate and transport of four contaminants in the San Joaquin River of California. The modeling results indicate that it took 20 days for these contaminants to transport from the upstream to the downstream in the research domain. These models can be effectively used for inland surface water restoration and management.
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