In this paper, the improved version of the meshless singular boundary method (ISBM) is developed for analyzing the hydrodynamic performance of bottom-standing submerged breakwaters in regular normally incident waves. Both the single and dual prismatic breakwaters of rectangular and trapezoidal forms are examined. Only the impermeable breakwaters are considered in this study. The physical problem is cast in terms of the Laplace equation governing an irrotational flow and incompressible fluid motion with the appropriate mixed-type boundary conditions, and it is solved numerically using the ISBM. The numerical results are presented in terms of the hydrodynamic quantities of reflection and transmission coefficients. The values are first validated against the data of previous studies, computed, and discussed for a variety of structural conditions, including the height, width, and spacing of breakwater submergence. An excellent agreement is observed between the ISBM results and those of other methods. The breakwater width is found to feature marginal effects compared with the height. The present method is shown to accurately predict the resonant conditions at which the maximum reflection and transmission occur. The trapezoidal breakwaters are found to generally present a wide spectrum of reflections, suggesting that they would function better than the rectangular breakwaters. The dual breakwater systems are confirmed to perform much better than single structures.