Hydraulic characteristic is very essential to do any seepage modeling study for better understanding of the flow behavior through the soil. It was found in the literature, that seepage losses through the base of an irrigation canal effect significantly in the total volume of water flowing through it. The cracking occurs in concrete lined irrigation canal due to rise in water level and other environmental factors necessitate the use of flexible material like geo-synthetic on the canal surface instead of concrete. The main advantage of using this flexible material is that it eliminates the cracking phenomena and simultaneously reduces the seepage of water through canal to a considerable extent. To understand this, an effort was made by conducting a modeling study with the help of finite element based software SEEP/W. The study considers a two dimensional canal model to see the variation of seepage through the soil underneath the canal base and sides. In this work, the seepage variation was indirectly studied by observing the Pore Water Pressure (PWP) variation in the soil. The PWP changes with the change in the amount of water in the soil. The PWP for a saturated soil is positive, while for an unsaturated soil it belongs to negative range. The variation of PWP beneath the canal bed was noted and plotted against the depth. Based on this variation, the seepage losses for the lined and unlined canal were compared for different water head in the canal. The study indicates that there is a considerable influence of water head in the PWP variation. Also, application of liner in canal surface reduces the seepage losses which was confirmed by the high negative PWP.