This study develops an iterative dual BEM (Boundary Element Method) model for water wave scattering by breakwaters having perforated thin plates, which avoids setting artificial sub-domains near the thin plates and thus is very convenient to write general computer codes. In order to directly consider the effect of wave height on the wave energy dissipation by perforated plates, a quadratic (nonlinear) pressure drop condition is imposed on the plates. Then, iterative calculations are conducted to solve the nonlinear boundary condition in the dual BEM model. Also, an analytical method to calculate the integrals of kernel function, which is generated from the hypersingular boundary integral equation in the dual BEM model, is introduced to enhance the calculation efficiency and accuracy. Numerical results show that the iterative calculations in the newly developed dual BEM solution converge rapidly. As examples, wave scattering by several typical breakwaters involving perforated thin plates are solved using the iterative dual BEM model. The corresponding numerical results of the reflection and transmission coefficients are in excellent agreement with the predictions by the analytical solutions. The numerical results also agree reasonably well with experimental data in literature. The present iterative dual BEM model is valuable for analyzing the hydrodynamic performance of breakwaters with perforated thin plates in preliminary engineering design.