Characterizing the spatio-temporal distribution of groundwater-surface water (GW-SW) exchange fluxes is of paramount importance in understanding catchment behavior. A wide range of field-based techniques are available for such characterization. The objective of this study is to quantify the spatio-temporal distribution of the exchange fluxes along the cakit stream (Nigde, Turkey) through coupling a set of geophysical techniques and in-stream measurements in a hierarchical manner. First, geological and water quality information were combined at the catchment scale to determine key areas for reach-scale focus. Second, electromagnetic induction (EMI) surveys were conducted along the reach to pinpoint potential groundwater upwelling locations. EMI anomalies guided our focus to a 665 m-long reach of the stream. Along this selected reach, a fibre-optic distributed temperature sensing (FO-DTS) system was utilized to investigate streambed temperature profiles at fine spatial and temporal scales. Furthermore, vertical hydraulic gradients and exchange fluxes were investigated using nested piezometers and vertical temperature profiles, respectively, at two potential upwelling locations and a potential downwelling location identified by previous surveys. The results of the study reveal heterogeneity of vertical water-flow components with seasonal variability. The EMI survey was successful in identifying a localized groundwater upwelling location. FO-DTS measurements revealed a warm temperature anomaly during cold air temperature and low streamflow conditions at the same upwelling site. Our point-based methods, namely vertical temperature profiles and vertical hydraulic gradient estimates, however, did not always provide consistent results with each other and with EMI and FO-DTS measurements. This study, therefore, highlights the opportunities and challenges in incorporating multi-scale observations in a hierarchical manner in characterization of the GW-SW exchange processes that are known to be highly heterogeneous in time and space. Overall, a combination of different methods helps to overcome the limitations of each single method and increases confidence in the obtained results.