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Field observation and numerical simulations were carried out to evaluate the hydraulic relationship between the shallow and deep aquifer of a High Plains Aquifer system, in which shallow and deep aquifers are separated by an aquitard. Pumping from the lower aquifer resulted in a small drawdown in the upper aquifer and a larger drawdown in the aquitard; pumping from the shallow aquifer caused a small drawdown in the aquitard and the deep aquifer. Analysis of pumping test data gives the values of the hydraulic conductivity of the aquitard and the deep aquifer. Long-term observation of groundwater levels in the shallow and deep aquifers showed that a strong downward hydraulic gradient was maintained during an irrigation season. Numerical simulations were used to calculate the induced leakage of water from the shallow to the deep aquifer. Water budget analyses suggested that after pumping continues for a couple of days, the leakage from the overlying layers begins to supply the majority of the withdrawal from the deep aquifer. However, the induced leakage from the upper shallow aquifer can travel only a few meters into the aquitard, and it can not reach the lower aquifer during a 90 day pumping period. The major portion of the induced leakage occurred during the pumping period, but a small leakage can continue as a residual effect after the pumping period. The vertical hydraulic conductivity of the aquitard plays a major role in partitioning the ratio of the induced leakage for the pumping and after-pumping periods.