A two-dimensional numerical groundwater flow model was established and calibrated for the hyperarid Najd region in southern Oman. The results indicate that recent recharge rates are required to sustain the observed groundwater heads in the Najd. The model was also used to estimate possible ranges of past recharge rates and the effective porosity of the main aquifer unit. Recharge rates during past humid periods were estimated to be no more than 1–3 times modern rates. The effective porosity was estimated to be between 0.06 and 0.093. Insight into the nature of the long-term transport within the aquifer was gained by using transient model runs over the last 350 ka and (1) varying the recharge intensity (from 0.1 to 2.5 times modern), and (2) the timing and duration of humid and dry periods. Finally, results indicate that although recharge rates and the flow conditions have likely changed over time, a steady-state model is capable of reproducing the observed groundwater residence times in the Najd based on carbon-14, helium and chlorine-36 dating.