In the water retaining structure, seepage through the body wall and foundation plays a major role in the failure of structures. To design any kind of structure for proper retaining, the effect due to seepage should be considered widely. In this paper, % of increase in arrested seepage is arrived from various analyses. Compressive strength of nano silica, nano alumina and carbon nano tube is found out by the experiment and Elastic modulus is calculated. Stress analysis is carried out with analysis software 3D SOLID WORKS. The critical location of the crack is noticed for various service conditions like water filled for full height (hd), more than half height (0.75hd) and half height (0.5hd). The seepage analysis is carried out on the basis of two-dimensional Laplace equations. The partial differential equation (PDE) Toolbox in MATLAB, by the method of finite element method (FEM), provides a powerful and flexible environment for the seepage study. Values of the velocity contours are recorded for various sizes of the crack at the critical location before treatment. Later, these cracks are filled with the mortar of nano-silica, nano alumina and carbon nano tube. The values of the velocity contours are recorded again after the treatment. Finally, the percentage increase in arrested seepage is calculated and it is found that carbon nano tube has behaved better.