Several hydrological models that are used for simulating the water flow in rivers and channels are based on the shallow water equations as in Copeland and El-Hanafy, (2006) or Saint Venant equations (El-Hanafy and Copeland, 2007a). Both the shallow water equations and the Saint Venant equations form a system of partial differential equations which presents mass and momentum conservation along the channel and include source terms for the bed slope and bed friction. This paper presents a staggered finite difference scheme for the channel routing based upon Saint Venant equations and the well know method of characteristics after modifying it to suit the case of a shallow water depth initially followed by a flood event (El-Hanafy and Copeland, 2007b). The modified method of characteristics is implemented to achieve a transparent down stream boundary. The relation between the water depth and the infiltration rate have been derived for Saint Venant equations and it is concluded that the effect of water stage have a positive effect on the infiltration rate as it was expected