Seepage problem and channel transition efficiency is one of the most important issues in managing and exploiting irrigation networks. Seepage rate should be minimized in the design and construction of irrigation channels. Anyway several methods have been represented to calculate seepage rate. Some methods that are numeral have their own complexity, and some methods are empirical. Due to the fact that the nature of the flow in the channels and the seepage of the walls are spatially varied flow, in this study, the governing dynamical equation is used and combined with the Chahar and Swamee equation. The final differential equation is solved by finite difference method (FDM), and the depth and flow rates of different cross sections of a channel are obtained. From the difference of flow rate in two cross sections, the seepage flow rate can be calculated. The information required for this method is the flow rate and flow depth at a downstream control channel, the hydraulic conductivity of the channel bed, the geometric characteristics of the channel, and the distance between the water table and the bottom of the channel. This model can be used for calculation of the transmission efficiency too.