The fraction of rain that is annually recharged to ground water is a function of the transient quantities of precipitation (wet vs. dry years) as well as other meteorological and geologic factors, and thus it is very difficult to estimate. In this study, we have used long records (20 to 30 years) of precipitation and spring discharge to reconstruct the transient character of yearly recharge. These data sets were used to calibrate numerical ground water flow models on the less than 3 km2 scale for four separate perched karstic aquifers in the Judean and Samarian Mountains of Israel. The stratification and karstic character of the local carbonate rock aquifers cause ground water to flow through discrete dissolution channels and to discharge at isolated springs. An innovative, dual-porosity approach was used where a finite-difference solution simulates flow in the rock matrix, while the karstic channels are simulated using computationally simple drains. Perched conditions are also simulated innovatively using MODFLOW by treating the bottom unsaturated layer as if it is saturated, but by assuming zero pressure head throughout the "unsaturated" layer. Best fitting between measured and computed spring hydrograph data has allowed us to develop a set of empirical functions relating measured precipitation to recharge to the aquifer. The generic methodology presented gives insight into the suspected changes in aquifer recharge rates between particularly wet or dry years.