Multiple submerged breakwaters (MSBWs) are commonly used coastal protection structures due to their specific advantages over the emerged ones. Rip currents, as the inevitable natural hazard in the gaps of these constructions, are investigated numerically in the present study. A fully nonlinear mild-slope equation (NMSE) model possessing both fully nonlinear and fully dispersive properties is validated and adopted in the simulations. With four monochromatic wave conditions of different wave heights, periods and incidences representing low-energy, typical, storm and oblique waves tested, the flow patterns and the low-frequency oscillations of the rip currents are studied. For the convenience of risk assessment, the rip risk level is divided into three degrees according to the maximum rip flow speed. The effects of the configurations of the MSBWs on the rip current system as well as the rip risk level are examined, considering different breakwater widths, heights, forms, gap widths and gap numbers. Simulation results suggest that the cross-shore configurations of MSBWs influence the rip risk level by inducing different wave energy dissipations but the longshore configurations of MSBWs by changing flow field patterns.