When estimating groundwater recharge in karstified and fractured aquifers it’s important to take into consideration, that they differ from porous aquifers by inhomogeneities of their hydraulic properties because of the great variance of infiltration properties in their rocks. In this research the process of groundwater recharge in Sher-mansour and Haramon areas in Antilebanon, where karstified and fractured aquifers are developed, was discussed. The portion of rainfall reaching the groundwater was calculated by applying water balance and groundwater level changes methods. In the first method the area was divided into surface zones and water balance components were calculated in each zone and the portion was estimated at 55.8% of rainfall in dry years like 2005-2006. In the second method the area was divided into subsurface zones and groundwater level fluctuations, storage coefficient and groundwater storage were calculated. The groundwater recharge varied between 17.5% in Haramon area and 80% in Sher Mansour area. The results showed that portions of rainfall reaching groundwater are not equal in the deferent subsurface zones and are deferent from those calculated by water balance method.