Root water uptake (RWU) by plants is one of the key processes controlling water, carbon and energy transfer within soil-plant-atmosphere systems. RWU from deeper portions of the soil profile is of vital importance in meeting atmospheric transpiration demand in water-limited environments, especially for plants that have direct access to groundwater. However, simulating the dynamic response of RWU, where water uptake is enhanced in unstressed parts of the root zone to compensate for stress in other soil regions is challenging and largely untested in ecosystem models because the distribution of RWU is commonly specified a priori. Here, we investigate the potential impacts of root length density (RLD) distributions and RWU compensation on transpiration and net primary productivity for maize in southern Wisconsin. An agroecosystem model that is capable of simulating variably saturated water flow in the unsaturated zone was driven with 27 years of hourly weather observations for various maize RLD distributions across a continuum of groundwater depths. The results show that plants with shallow RLD can utilize up to twice as much groundwater as the plants with deep RLD if the water table is near the root zone. Furthermore, the RWU compensation substantially reduces (up to 75%) the groundwater dependency of plants with deep RLD in comparison to shallower rooted plants. Moreover, plant root structure and RWU strategy controls the strength of the relationship between groundwater depth and transpiration in the critical water table range. Transpiration is progressively more sensitive to the groundwater levels as RLD becomes shallower and plants using compensated RWU are less sensitive to groundwater depths regardless of their root structure during dry years. Our findings underscore the importance of incorporating compensatory RWU in agroecosystem models to account for highly variable climate and groundwater depth conditions.