Two key challenges regarding the design and operation of aquifer recharge and recovery (ARR) systems are evaluating aquifer heterogeneity and understanding hydrochemical interactions. Uncertainty in this respect can impact the volume of recoverable water and the improvement in water quality. The objective of this research is to leverage the advantages of geophysical measurements and hydrochemical sampling to reveal the properties of an ARR site to inform current ARR system operations and future design decisions. Electrical resistivity tomography was used to image the subsurface below two key infiltration/extraction areas of an ARR site in Colorado, USA. Hydrochemical measurements on transects intersecting the geophysical measurements resolved bulk parameters (i.e., total organic carbon, nitrate, and major cations and anions) and trace organic chemicals (e.g., pharmaceuticals, personal care products). Conservative tracers were also used to estimate degrees of mixing and water travel times and to better assess the performance of the ARR site regarding water quality changes and water recovery. The electrical resistivity measurements suggest that certain areas of the infiltration basins have hydraulic connections to the extraction wells through preferential flow paths, compared with other infiltration basins that are separated by fine-grained materials from their respective extraction wells. The hydrochemical results indicate that consistent improvements in water quality can be achieved in these preferential flow paths within relatively short travel times (<5 d) at this ARR site.