Line-by-line (LBL) solution method is a numerical and semidirect method, which can be applied for solving algebraic equation set resulted from discretization. In this article, the effect of solution arrangement of the grids (SAG) on accuracy of diffusion equation's solution has been investigated. First of all, diffusion equation had been discrete by finite volume method; in the second place, MATLAB software has been exploited for writing a code for solving algebraic equation set by using LBL solution method with alternative SAG. In the third place, for examining the effect of SAG, water seepage through foundations of several concrete dams was modeled with this code. In addition, these dams were modeled in SEEP/W 2004 and PHASE2 6.0 software, as support. Finally, we drew an analogy between the results by Mann–Whitney U statistical test with SPSS 14 software. Comparison of the results revealed that SAGs have affected P-value up to 39%. As a result, the most accurate SAGs had been decided by the problem geometry. Furthermore, the result of the finite volume and finite element methods had no statistical by significant difference. Moreover, convergence and convergence path had been dictated by problem geometry and SAGs.