3D-fluorescence spectroscopy was used as a monitoring tool to describe the fate and transport of dissolved organic matter (DOM) during groundwater recharge using recycled water, imported water, and stormwater at a managed aquifer recharge site in California. The study was supplemented by analysis of conservative wastewater-derived trace organic chemicals using liquid chromatography coupled with tandem mass spectrometry. Parallel factor analyses (PARAFAC) yielded six different independent fluorophoric components by mathematically decomposing the excitation emission spectra. The results revealed that this approach was successful in showing the decrease of chromophoric DOM in the subsurface over time and distance during recharge and detecting anthropogenic contaminations that were introduced into the recharge basins, most likely from weed and vector control applications. PARAFAC was able to extract at least one herbicide with chromophoric features from surface and groundwater excitation-emission matrices, suggesting that this approach could also be applied as a pollution control tool for hazardous events.