In the present work, the improved version of the meshless singular boundary method (ISBM) is developed for analyzing the performance of bottom standing submerged permeable breakwaters in regular normally incident waves and in the proximity of a vertical wall. Both single and dual prismatic breakwaters of rectangular and trapezoidal forms are examined. The physical problem is cast in terms of the Laplace equation governing an irrotational flow and incompressible fluid motion with appropriate mixed type boundary conditions, and solved numerically using the ISBM. To model the permeability of the breakwaters fully absorbing boundary conditions are assumed. Numerical results are presented in terms of hydrodynamic quantities of the reflection coefficients. These are firstly validated against the results of a multi-domain boundary element method (BEM) developed independently for a previous study. The agreement between the results of the two methods is excellent. The coefficients of reflection are then computed and discussed for a variety of structural conditions including the breakwaters height, width, spacing, and absorbing permeability. Effects of the proximity of the vertical plane wall are also investigated. The breakwater's width is found to have only marginal effects compared with its height. Permeability tends to decrease the minimum reflections. These coefficients show periodic variations with the spacing relative to the wavelength. Trapezoidal breakwaters are found to be more cost-effective than the rectangular breakwaters. Dual breakwater systems are confirmed to perform much better than single structures.