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Marine hydrokinetic (MHK) projects will extract energy from ocean currents and tides, thereby altering water velocities and currents in the site's waterway. These hydrodynamics changes can potentially affect the ecosystem, both near the MHK installation and in surrounding (i.e., far field) regions. In both marine and freshwater environments, devices will remove energy (momentum) from the system, potentially altering water quality and sediment dynamics. In estuaries, tidal ranges and residence times could change (either increasing or decreasing depending on system flow properties and where the effects are being measured). Effects will be proportional to the number and size of structures installed, with large MHK projects having the greatest potential effects and requiring the most in-depth analyses. This work implements modification to an existing flow, sediment dynamics, and water-quality code (SNL-EFDC) to qualify, quantify, and visualize the influence of MHK-device momentum/energy extraction at a representative site. New algorithms simulate changes to system fluid dynamics due to removal of momentum and reflect commensurate changes in turbulent kinetic energy and its dissipation rate. A generic model is developed to demonstrate corresponding changes to erosion, sediment dynamics, and water quality. Also, bed-slope effects on sediment erosion and bedload velocity are incorporated to better understand scour potential.