This research paper presents a simulation study to predict the percolation of water through soil liners using numerical modeling with HYDRUS-2D. The soil liners included compacted clay/sand mixtures of 0 to 25% clay at 5 to 30 cm thickness. The cumulative water flux or hydraulic barrier at drain layer at the end of simulation period reached a ratio of 0.81, 0.54, 0.29 and 0.09 of water flux at a top profile with no soil liner. The soil liners of 25 and 30 cm thickness with 20% and 15% clay had lesser percolation or water flux at drain layer by about 0.21 and 0.44 compared to water flux at top layer with no soil liner. Using a modeling approach efficient liner systems can be designed for use in water harvesting projects or landfill covers. The modeling and simulation are dependent on the hydraulic conductivity of the compacted soil liner, soil water characteristics curves as well as irrigation and rainfall rates.