Small island developing states are among the most vulnerable areas to the impact of natural hazards and climate change. Flooding due to storm surges and extreme waves, coastal erosion, and salinization of freshwater lenses are already a serious threat and could lead to irreversible consequences in the coming decades. Reef flat mining is one of the most common practices to source the required material for the implementation of coastal protection measures, but concerns remain that partial removal of the protective reef could increase wave loading on the islands. However, the available data and knowledge on the effects of these mining pits are currently very limited. This study provides new insights on the effects that pits may have on nearshore hydrodynamics and wave runup. Results are based on a large numerical data set of fringing reefs, derived using the validated XBeach nonhydrostatic+ process-based model. Model results indicate that excavation pits cause a decrease in infragravity wave energy around the fundamental mode of the reef, which is partly caused by reduced wave transmission. Additionally, changes in sea and swell wave energy are attributed to reduced transmission, “a decrease” in wave dissipation, and (triad) wave–wave interaction. Furthermore, in 13% of all modeled cases, an increase in wave runup is observed, mainly due to more sea and swell wave energy reaching the shoreline. This probability is lowest for narrow pits relative to the reef flat width or pits located further from shore.