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Groundwater use for irrigation has a major influence on agricultural productivity and local water resources. This study evaluated the groundwater irrigation schemes, SWAT auto-irrigation scheduling based on plant water stress (Auto-Irr), and prescribed irrigation based on well pumping rates in MODFLOW (Well-Irr), in the U.S. Northern High Plains (NHP) aquifer using coupled SWAT-MODFLOW model simulations for the period 1982–2008. Auto-Irr generally performed better than Well-Irr in simulating groundwater irrigation volume (reducing the mean bias from 86 to −30%) and groundwater level (reducing the normalized root-mean-square-error from 13.55 to 12.47%) across the NHP, as well as streamflow interannual variations at two stations (increasing NSE from 0.51, 0.51 to 0.55, 0.53). We also examined the effects of groundwater irrigation on the water cycle. Based on simulation results from Auto-Irr, historical irrigation led to significant recharge along the Elkhorn and Platte rivers. On average over the entire NHP, irrigation increased surface runoff, evapotranspiration, soil moisture and groundwater recharge by 21.3%, 4.0%, 2.5% and 1.5%, respectively. Irrigation improved crop water productivity by nearly 27.2% for corn and 23.8% for soybean. Therefore, designing sustainable irrigation practices to enhance crop productivity must consider both regional landscape characteristics and downstream hydrological consequences.