Combining geochemical data with physical data produces a powerful method for understanding sources and fluxes of waters to river systems. This study highlights this for river systems in regions of complex hydrogeology, shown here through the identification and quantification of base-flow sources to the Verde River and its tributaries within the middle Verde River watershed. Specifically, geochemical tracers (major solutes, stable and radioactive isotopes) characterize the principal aquifers (C, Redwall-Muav, and Verde Formation) and provide a conceptual understanding of the hydrologic connection between them. For the surface-water system, PCA is utilized to identify potential base-flow sources to the Verde River on a several-kilometer scale. Solute mixing diagrams then provide relative inputs of these sources, and when combined with stream discharge, allow for quantification of water sources. The results of this study provide an improved conceptual model that reveals the complexity of groundwater-surface water exchanges in this river basin.