Wave breaking on the steep fore-reef slopes of shallow fringing reefs is effective at dissipating incident sea-swell waves prior to reaching reef shorelines. However, wave setup and free infragravity waves generated during the sea-swell breaking process are often the largest contributors to wave-driven water levels at the shoreline. Laboratory flume experiments and a multi-layer phase-resolving nonhydrostatic wave-flow model, which includes a canopy model to predict drag forces generated by roughness elements, were used to investigate the wave-driven water levels on fringing reefs. Though the model is capable of three dimensional simulations, consistent with the laboratory study, a two-dimensional vertical mode was used. In contrast to many previous studies, both the laboratory experiment and the numerical model account for the effects of large bottom roughness. The numerical model reproduced the observations of the wave transformation and runup over both smooth and rough reef profiles. The numerical model was then extended to quantify the influence of reef geometry and compared to simulations of plane beaches lacking a reef. For a set offshore forcing condition, the fore-reef slope controlled wave runup on reef fronted beaches, whereas the beach slope controlled wave runup on plane beaches. As a result, the coastal protection utility of reefs is dependent on these slopes. For our examples, with a fore-reef slope of 1/5 and a 500 m prototype reef flat length, a beach slope of ~1/30 marked the transition between the reef providing runup reduction for steeper beach slopes and enhancing wave runup for milder slopes. Roughness coverage, spacing, dimensions, and drag coefficient were investigated with results indicating the greatest runup reductions were due to tall roughness elements on the reef flat.