Groundwater has been an important source for agriculture irrigation in the High Plains Aquifer Region and caused decreasing stream flow since the 1950s. Irrigation return flow complicates the stream depletion problem, as it partially offsets the flow decrease caused by groundwater pumping. The stream flow recorded at stream gauges is a composite consequence from the dynamic interactions between surface water (SW) and groundwater (GW) systems, which have been aggravated by human activities. This study examines the complexity through a modified version of Soil and Water Assessment Tool (SWAT). An aquifer storage component is modified to the original SWAT, which allows the model to simulate the complicating effects of groundwater pumping and irrigation return flow on natural stream flow. The model is applied to the Frenchman Creek Basin, Nebraska. Results show that intensive pumping reverses the natural seasonal groundwater recharge pattern, from «summer recharge and winter discharge» under natural conditions to «summer discharge and winter recharge» under the human interferences. The irrigation-induced flow becomes a considerable portion of stream flow during the crop-growing season, implying that fluvial ecosystems may rely on return flows and be affected by irrigation practices. Conjunctive surface and ground water management has the potential to balance irrigation requirement and environmental flow conservation.