For the karst aquifer in the background of the Vipava springs in south-western Slovenia the first the model of the recharge estimation was set on the base of the method of soil moisture balance. Additional to precipitation, the influences of the interception on vegetation cover, snow and snowmelt, evapotranspiration, water storage in soil, rapid recharge and secondary infiltration were also considered in this model. It was calibrated by comparison with the discharges of the Vipava springs and then the daily values of recharge were estimated. To test the role of such accurate estimation of the recharge in further hydrodynamic analysis of karst aquifers, the black-box method was used. As the input signal in the supposed linear system the measured precipitation was first adopted, and then the estimated recharge values. It was demonstrated by comparison of results that the introduction of the recharge function significantly improves the model. In this way the important influence of the processes in the air, vegetation and soil on the amount and the time distribution of the recharge, and through this also on the hydrodynamic functioning of karst aquifers, was proved.