Few studies have investigated large reaches of rivers in which multiple sources of groundwater are responsible for maintaining baseflow. This paper builds upon previous work undertaken along the Fitzroy River, one of the largest perennial river systems in north-western Australia. Synoptic regional-scale sampling of both river water and groundwater for a suite of environmental tracers (4He, 87Sr/86Sr, 222Rn and major ions), and subsequent modeling of tracer behavior in the river, has enabled definition and quantification of groundwater input from at least three different sources. We show unambiguous evidence of both shallow "local" groundwater, possibly recharged to alluvial aquifers beneath the adjacent floodplain during recent high-flow events, and old "regional" groundwater introduced via artesian flow from deep confined aquifers. We also invoke hyporheic exchange and either bank return flow or parafluvial flow to account for background 222Rn activities and anomalous chloride trends along river reaches where there is no evidence of the local or regional groundwater inputs. Vertical conductivity sections acquired through an airborne electromagnetic (AEM) survey provide insights to the architecture of the aquifers associated with these sources and general groundwater quality characteristics. These data indicate fresh groundwater from about 300 m below ground preferentially discharging to the river, at locations consistent with those inferred from tracer data. The results demonstrate how sampling rivers for multiple environmental tracers of different types-including stable and radioactive isotopes, dissolved gases and major ions-can significantly improve conceptualization of groundwater-surface water interaction processes, particularly when coupled with geophysical techniques in complex hydrogeological settings.