[Purposes] The construction of wave-sheltering structures near reef islands can alter the wave and flow boundary conditions, resulting in significant impacts on the hydrodynamic fields around these reef-channel-island systems. [Methods] In this study, a non-hydrostatic wave numerical model, SWASH, was utilized to simulate the wave-induced circulation and vorticity fields around constructed islands and reefs. [Findings] The results show that the breakwaters have a significant influence on the flow velocities within the model region. As the breakwater length increases and the distance between the breakwaters decreases, the overall flow velocity within the model region decreases, and the transverse variations within the cross-sections become smaller. The maximum onshore and cross-shore flow velocities above the reef platform increase with an increasing distance between the breakwaters. When the breakwaters are positioned closer to the rear of the reef platform and are shorter in length, the onshore flow velocity within the gap approaches the velocity when there is no breakwater. The maximum vorticity value within the model does not significantly vary with changes in the breakwater length and distance between breakwaters, but is consistently located at the tail of the breakwater. [Conclusions] This model effectively simulates the flow field around island and reef systems with constructed breakwaters, providing scientific evidence for the design and construction of breakwaters in complex flow environments.