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This data set consists of physics-based Delft3D-FLOW and SWAN hydrodynamic models input files used to study the wave-induced 3D flow over spur-and-groove (SAG) formations. SAG are a common and impressive characteristic of coral reefs. They are composed of a series of submerged shore-normal coral ridges (spurs) separated by shore-normal patches of sediment (grooves) on the fore reef of coral reef environments. Although their existence and geometrical properties are well documented, the literature concerning the hydrodynamics around them is sparse. Here, the three-dimensional flow patterns over SAG formations, and a sensitivity of those patterns to waves, currents, and SAG geometry were examined. Shore-normal shoaling...