Abstract In Hawaiʻi and other Pacific high islands submarine groundwater discharge (SGD) can be a significant and continuous source of solutes to nearshore reefs and may play a key role in the structure and function of benthic coral and algal communities. Identifying SGD sources and linking them to reef biogeochemistry is technically challenging. Here we analyzed spectra of fluorescent dissolved organic matter (fDOM) in coral reefs in the context of a suite of biogeochemical parameters along gradients of SGD to characterize fDOM composition and evaluate the utility of fDOM signatures in tracking groundwater dispersal and transformation. We spatially mapped water column chemistry in Maunalua Bay, O‘ahu, Hawaiʻi by collecting 24 water samples in grids at each of two ~ 0.15 km2 regions during both high and low tides over a two-day period. We observed clear horizontal gradients in the majority of 15 measured parameters, including inorganic and organic solutes and organic particles that tracked concentrations of conservative SGD tracers (radon, salinity and silicate). Multivariate scanning excitation-emission fluorometry successfully differentiated two distinct groundwater sources and delineated regions of SGD dispersion in each reef from the surrounding water column samples without detectable groundwater. Groundwater was consistently depleted in DOC and enriched in nutrients; although the two SGD sources varied widely in fDOM quantity and fluorophore proportions, indices of humification were consistently elevated in SGD at both sites. Our results provide a robust spectral characterization of fDOM in SGD-influenced coral reefs and indicate the potential for this rapid and cost-effective measurement technique to be useful in tracking SGD dispersal in nearshore ecosystems.