The interaction between surface water and groundwater is recognized as a key process for effective management of water resources. However, scale dependency and spatial heterogeneity of the processes at the interface are limiting factors in the characterization of this process. A hierarchical, multi scale methodology has been devised and demonstrated to effectively and efficiently characterize the surface water-groundwater interaction along a 2-km reach in Kirmir stream, Turkey. Our methodology starts with investigation of geological information at the regional scale. At the intermediate scale, thermal infrared imagery is utilized to pinpoint groundwater seepage locations. Discharge measurements helped to understand the gains/losses. Point scale measurements including vertical hydraulic gradients, streambed vertical/horizontal temperature profiles and electrical conductivity profiles are investigated to characterize spatio-temporal variation in the vertical fluid fluxes. The results indicated that the study reach can be separated into three sections; upstream loosing section, downstream gaining section and mid-section with a seasonally variable character. Moreover, dam operation was found to control the exchange process a rapid rise in the river stage resulted in temporary reversal of the exchange processes. Analysis of chloride concentrations indicated that the lower confined aquifer is likely the source for the seepage at a fault-controlled section of the streambed.