From a critical zone perspective, the present paper aims to present the magnitude of groundwater recharge under different agricultural land-use types, reveal the process of water and solute transport in thick vadose zone, evaluate the “time lag” effect of recharge, and underscore the role of thickening vadose zone in recharge. The results indicated that different agricultural land-use types need to be further considered in recharge rate estimate. Under the typical irrigation condition in the piedmont plain, the recharge rate under flood irrigated winter wheat and summer maize (W/M_F), maize (M), non-cultivation (NC), native vegetation (NV), vegetables (V), and orchards (O) is 206.4, 149.7, 194.1, 46.4, 320.0, and 48.6 mm/yr, respectively. In the central plain, the value under W/M_F, M, NC, V, and cotton (C) is 92.8, 50.8, 85.0, 255.5, and 26.5 mm/yr, respectively. Soil water residence time (several years) and groundwater level response time (several months) should be distinguished to further understand the processes of groundwater recharge, because the soil water displacement velocities range from 0.2 to 2.2 m/yr while the rate of wetting front propagation is approximately 47 m/yr in the piedmont plain. The thickening vadose zone would prolong residence time of soil water and contaminant, which could postpone the time of or alleviate groundwater pollution, but have no significant influence on the magnitude of recharge in a long time scale. Recharge coefficient based on shorter time span (e.g. 2 or 3 years) should be used with caution as a parameter for groundwater resources evaluation, because it varies with total water input and target soil depth. Uncertainties in evapotranspiration and other water balance components should be evaluated in recharge estimation and the impact of land-use types on recharge should be emphasized. The critical zone science would greatly improve the understanding of groundwater recharge processes. The results of the present study will be helpful in sustainable groundwater resources management.