Measurements taken by the Gravity Recovery and Climate Experiment satellites indicated a continued water storage increase over the Missouri River Basin (MRB) prior to the 2011 flood event. An analysis of the major hydrologic variables in the MRB, i.e., those of soil moisture, streamflow, groundwater storage, and precipitation, show a marked variability at the 10–15 year time scale coincident with the water storage increase. A climate diagnostic analysis was conducted to determine what climate forcing conditions preceded the long-term changes in these variables. It was found that precipitation over the MRB undergoes a profound modulation during the transition points of the Pacific quasi-decadal oscillation and associated teleconnections. The results infer a prominent teleconnection forcing in driving the wet/dry spells in the MRB, and this connection implies persistence of dry conditions for the next 2 to 3 years.