Since surface water and groundwater systems are fully coupled and integrated systems, increased groundwater withdrawal during drought may reduce groundwater discharges into the stream, thereby prolonging both systems’ recovery from drought. To analyze watershed response to basin-level groundwater pumping, we propose an uncertainty framework to understand the resiliency of groundwater and surface water systems using a fully-coupled hydrologic model under transient pumping. The proposed framework incorporates uncertainties in initial conditions to develop robust estimates of restoration times of both surface water and groundwater systems and quantifies how pumping impacts state variables such as soil moisture. Groundwater pumping impacts over a watershed were also analyzed under different pumping volumes and different potential climate scenarios. Our analyses show that groundwater restoration time is more sensitive to variability in climate forcings as opposed to changes in pumping volumes. After the cessation of pumping, streamflow recovers quickly in comparison to groundwater, which has higher persistence. Pumping impacts on various hydrologic variables were also discussed. Given that surface water and groundwater are inter-connected, optimal management of the both resources should be considered to improve the watershed resiliency under drought. Potential for developing optimal conjunctive management plans using seasonal-to-interannual climate forecasts is also discussed.