In drier regions, accurate knowledge of groundwater recharge is important for the sustainable management of scare water resources. Thirunelvely in Jaffna Peninsula is an area where groundwater is being utilized for domestic, agricultural and municipal water supply. Further the groundwater in this area also contaminated with nitrogenous fertilizer application due to intensive agriculture, as post war conditions in the Peninsula encourage farmers to engage in intensive agricultural activities. Very few or no studies have been conducted in the recent past on groundwater recharge or solute transport such a fertilizer leaching in this area. HYDRUS-1D is a Windows-based modelling environment for analysis of water flow and solute transport in variably saturated porous media. HYDRUS-1D is just as quick and cheap as other soil moisture balance models but more physically based and flexible as it allows for building up complexity as data are available whether for solute transport or non-equilibrium flow etc. Therefore the main objective of this paper is to simulate potential groundwater recharge using HYDRUS-1D and compare it with the results obtained in Thirunelvely using soil moisture balance and water table fluctuation methods. Results have shown that the HYDRUS-1D simulated potential groundwater recharge (41.8 cm) has close agreement with that estimated by other methods with high coefficient of determination (R 2 = 0.95). Further runoff, soil moisture storage and bottom pressure head simulated by HYDRUS-1D too have good agreement with field observation. Therefore HYDRUS-1D is capable of simulating potential groundwater recharge close to the previously estimated values in Thirunelvely as it has good agreement with the water table fluctuation measured in the study site and the bottom head pressure at the 1 m soil profile simulated in the HYDRUS-1D model. Now that it has been demonstrated that HYDRUS-1D adequately reproduces the water fluxes predicted by other C S. De Silva 44 methods, it could be used for groundwater recharge with more confidence and to investigate pollution in soil zone and groundwater.