This study numerically investigates wave transformation and setup processes across fringing reefs, focusing on artificial reef configuration effects under varying tidal conditions and incident wave parameters. The OpenFOAM-based waves2Foam model simulates hydrodynamic processes along reef profiles containing a fore-reef slope and reef flat. Following validation against laboratory data, the model simulates cross-shore wave height attenuation and setup within fringing reef systems. The results demonstrate that reef flat water depth substantially modulates wave dynamics: during low tide, intensified wave breaking elevates the maximum wave height and setup by up to 45.7% and 78.5%, respectively, compared to high-tide conditions. Furthermore, this water depth critically governs the reef configuration’s influence on wave energy dissipation efficiency. Under high tide, additional reef rows increase the peak wave height by 5.2% while reducing wave setup by 10.5%. In contrast, expanded reef spacing reduces the peak wave height by 2.1% and decreases the peak wave setup by 2.4%. The temporal evolution of wave reflection ($K_R$) and transmission ($K_T$) coefficients reveals that shallow-water conditions amplify wave reflection while diminishing transmission capacity, as tidal variations directly regulate wave propagation mechanisms through water depth modulation. At the outer reef flat boundary, $K_R$ and $K_T$ values for existing artificial reefs exhibit variations below 5% across all tidal phases, row configurations, and spacing combinations. Consequently, current reef structures provide limited control over wave transmission in fringing reef terrains, indicating that structural modifications such as increasing reef elevation or deploying reefs on the fore-reef slope could enhance attenuation performance.