Internal waves breaking on continental shelves play a significant role in mixing and nutrient delivery to coral reef ecosystems. As internal solitary waves, or solitons, propagate shoreward onto continental slopes, they can become unstable and break into turbulent bores that bring cool, nutrient-rich sub-thermocline water shoreward onto coral reefs. The propagation of turbulent bores generated by internal waves interacting with a complex surface creates high-frequency variabilities in the thermal and nutrient environment of Conch Reef in the Florida Keys, which has been studied previously. Here, I have created a three-dimensional model using ANSYS Fluent Computational Fluid Dynamics (CFD) software to simulate the interaction of breaking internal waves and the complex bottom topography of a well-studied spur and groove reef. Modeling the dispersion and retention of cold, nutrient-rich water on three-dimensional reef topography can increase our understanding of bathymetry-induced mixing from internal waves and how this plays a role in benthic community structure and a reef’s resilience to heat stress.