Two stream discharge gages were established in the main stem Scott River late July 2008. These gages were established to refine the understanding of the Scott River’s water balance and supply and further the investigations into the gaining and losing reaches and groundwater-surface water interactions in the main stem. The gages were not operated for the entire water year due to concerns about high winter flows and channel stability. The monitoring program successfully documented the period approaching low flow and base flow conditions at the two sites during WY2009. The Scott River was disconnected at both locations during the late summer and early fall of 20009. The period in which connectivity was returned in mid October 2009 following a significant precipitation event was documented. Comparison of the discharge timing and magnitude and daily accumulated volume of water (acre feet per day) documented at these two locations with the locations monitored by the USGS and the California Dept. of Water Resources provides a case study of a run off event that restores connectivity throughout the Scott River.