Riparian tree canopies are key components of river systems, and influence the provision of many essential ecosystem services. Their management provides the potential for substantial control of the downstream persistence of pollutants. The recent advent of new advances in mass spectrometry to detect a large suite of emerging contaminants, high-frequency observations of water quality and gas exchange (e.g., aquatic eddy covariance), and improved spatial resolution in remote sensing (e.g., hyperspectral measurements and high-resolution imagery), presents new opportunities to understand and more comprehensively quantify the role of riparian canopies as Nature-based Solutions. The paper outlines how we may now couple these advances in observational technologies with developments in water quality modelling to integrate simulation of eutrophication impacts with organic matter dynamics and fate of synthetic toxic compounds. In particular regarding solar radiation drivers, this enables us to scale-up new knowledge of canopy-mediated photodegradation processes at a basin level, and integrate it with ongoing improvements in understanding of thermal control, eutrophication, and ecosystem metabolism.