A fully automated online ultraviolet (UV) digestion method for subsequent mercury (Hg) quantification in humic matter containing river waters is reported. The new developed flow injection analysis system (FIAS) consists basically of a UV lamp, a meander-form quartz glass reaction tube for online irradiation of the sample, and a nano-gold collector for preconcentration of dissolved mercury species. The FIAS is coupled to an atomic fluorescence spectrometer (AFS) for Hg detection. The optimized procedure allows accurate mercury quantification in water samples with up to 15 mg C L−1 as dissolved organic carbon by addition of only 1% (v/v) of hydrogen peroxide solution and online UV irradiation for 6 min. Addition of strong oxidants and any other reagents is avoided due to the use of the catalytic active nano-gold collector. Here, preconcentration of Hg species, release of mercury as Hg0, and AFS measurement are performed without addition of any reagents. Hence, the proposed approach offers significant advantages over existing methods. Analytical figures of merit showed the good performance of the developed method: The limit of quantification was found to be as low as 0.14 ng Hg L−1. The linear working range is from 0.1 to 200 ng Hg L−1 and relative standard deviation is <6.0% (n = 9). The system was successfully validated by comparison of the mercury concentrations found in model and real water samples obtained by the reference method EPA 1631 and the proposed method. Furthermore, application to six real river waters confirmed the feasibility of the proposed approach.