The highly variable climate of the Red River Valley of the North brings both flood and drought conditions, leading to an interest in subsurface water management systems (WMS). These subsurface WMS can drain excess water from the soil profile through subsurface drainage (SSD), manage water tables through controlled drainage (CD), and add additional water through subirrigation (SI). The subsurface WMS used in this study included a 21 ha CD, 17 ha CD + SI, and 16 ha undrained (control) field over a clay loam and silty clay loam soil planted with corn (2013) and soybean (2014). Both SSD and contributions from a shallow WT, through upward flux (UF), were incorporated into the Checkbook method for Irrigation Scheduling. Over the 2013 and 2014 growing seasons, daily soil moisture deficit (SMD), estimated through the modified Checkbook method (SMDSSD,UF) produced similar, if not more accurate, estimations of daily SMD.