As recognized in the European Water Framework Directive, groundwater-dependent wetlands and their diverse ecosystems have important functions which need to be protected. The vegetation in such habitats is often dependent on quality, quantity and patterns of river discharge and groundwater-surface water interaction on a local or reach scale. Since groundwater-surface water exchange studies on natural rivers and wetlands with organic soils are scarce, more functional analysis is needed. To this end we combined different field methods including piezometer nests, temperature as tracer and seepage meter measurements. Some of these measurements were used as inputs and/or as validation for the numerical 1-D heat transport model STRIVE. In transient mode the model was used to calculate spatially distributed vertical exchange fluxes from temperature profiles measured at the upper Biebrza River in Poland over a period of nine months. Time series of estimated fluxes and hydraulic head gradients in the hyporheic zone were used to estimate the temporal variability of groundwater-surface water exchange. This paper presents a hierarchical approach for quantifying and interpreting groundwater-surface water interaction in space and time. The results for the upper Biebrza show predominantly upward water fluxes, sections of recharge, however, exist along the reach. The fluxes depend more on hydraulic gradients than on riverbed conductivity. This indicates that the fluvio-plain scale is required for interpreting the exchange fluxes, which are estimated on a local scale. The paper shows that a conceptual framework is necessary for understanding the groundwater-surface water interaction processes, where the exchange fluxes are influenced by local factors like the composition of the riverbed and the position of the measurement on a local scale, and by regional factors like the hydrogeology and topography on a fluvio-plain scale. The hierarchical methodology increases the confidence in the estimated exchange fluxes and improves the process understanding. The accuracy of the measurements and related uncertainties, however, remain challenges for wetland environments. Gaining quantitative information on groundwater-surface water interaction can improve modeling confidence and as a consequence helps to develop effective procedures for management and conservation of valuable groundwater dependent wetlands.