In the presence of the complex-hydrodynamic phenomenon, the previous studies on wave transmission characteristics behind low-crested submerged breakwaters are still insufficient yet to appropriately understand of their behaviour. Therefore, a reliable prediction through a computational fluid dynamic (CFD) approach of waves across the structure is necessarily required. This paper presents three-dimensional (3D) computational modelling on hydrodynamic performance of narrow crest behind submerged breakwater aimed at gaining a comprehensive insight into the wave transmission coefficient (Kt)(Kt) characteristics. Meanwhile, a two-dimensional (2D) analysis has been initially carried out to provide a satisfactory description of the fundamental hydrodynamic phenomena through capturing the patterns of wave surface profile, flow velocity, and wave energy dissipation. In addition, a numerical wave tank model is well developed on the basis of the extended Reynolds Average Navier–Stokes (RANS) solver incorporated with level set algorithm to treat highly nonlinear effects at interface boundary between water, air and porous obstacle. Here, a submerged breakwater called as wave breaker coral restorer (WABCORE) designed by the National Water Research Institute of Malaysia is then employed. Based on the capability of laboratory experiment, the tested wave parameters were properly selected in 1:4 scaled model of the breakwater for wave height ranging from 0.10 to 0.25 m and wave period ranging from 1.5 to 2.5 s, in which correspond to the recorded wave prototype characteristics at Island of Tinggi, Malaysia. Thus, the wave constraints on a regime of small wave height and wavelength were then considered for various relative significant incident wave height, wave steepness, relative structural crest width and water-depth and have been taken into account in the computational simulation of the transmission coefficient (Kt)(Kt). The result shows that a good agreement was obtained between numerical and experimental measurements. KtKt decreases to less than 0.5 with increasing relative water depth (0.40≤h/d≤1.000.40≤h/d≤1.00) for significant incident wave height (0.1338≤Hs/d≤0.55470.1338≤Hs/d≤0.5547), wave steepness (0.0164≤Hs/L≤0.13030.0164≤Hs/L≤0.1303), and crest width of breakwater (0.0256 ≤Cw/L≤0.0512≤Cw/L≤0.0512). Detailed investigation suggests that the result is attributed to significant wave transformation in the vicinity of breakwater, especially for higher h/d. Furthermore, the wave absorbing effect of the submerged WABCORE breakwater is markedly better for increased steepness of Hs/LHs/L from 0.0292 to 0.0204 at h/d=1.00h/d=1.00, which is consistent with the augmented turbulent energy and dissipation shown on CFD visualizations across the breakwater entanglement.