Many small island developing states (SIDS) are among the most vulnerable to climate change (e.g. sea level rise) and seasonal to inter-annual climate variability, and subsequently experience flooding due to swell waves and wind waves, coastal erosion and salinisation of freshwater lenses. To counteract this, reef flat mining for sand and aggregate offers a possible solution to the material demand for coastal protection infrastructure and other engineering projects. However, the knowledge on the effects of these pits is limited to only two studies at a single reef: near-shore wave transformation based on measurements (Ford et al., 2013) and a numerical modelling study (Yao et al., 2016). This MSc thesis provides insights on the effects of pits, related to hydrodynamics and wave runup, on a large variety of fringing reefs, by using a 1D and 2DH process-based wave-resolving hydrodynamic model (XBeach non-hydrostatic+, “XBnh+”). Model results indicate that excavation pits cause a decrease in amplitude for waves in the infra-gravity (IG) frequency band. For the majority of the modelled reefs, this was mainly due to a modification of the longest natural frequency of the reef caused by the pit, resulting in a decrease in resonant amplification. Both pit width and cross-shore location have a strong influence on this mechanism. The observed changes in variance in the high frequency (HF) band can be partly explained by a decrease in wave dissipation, as well as a decrease in wave-wave (triad) interaction, both associated with (locally) increased water depth, which causes an increase of the HF peak and a decrease of the HF tail. Of all modelled reefs, there is a 15% chance of an increase in wave runup due to the presence of a pit. This probability is lowest for pits with narrow width and/or located close to the reef crest. The change in runup ranges from +10% to -20%. An increase in runup is caused by a combination of increased wave energy at peak frequencies, as well as smaller reductions in resonant amplification. Moreover, the effects of pits on mean water level near-shore of the excavation can cause circulation patterns that potentially result in coastal erosion and entrapment of sediments.