Natural dissolved organic matter (DOM) is composed of a variety of organic compounds, which can interact with metals in aquatic environments. The interactions between DOM and two metals of environmental concern (Cu(II) and Hg(II)) were studied using fluorescence quenching titrations combined with excitation-emission matrix (EEM) spectra and parallel factor analysis (PARAFAC). This allowed characterizing the specific interactions between eight fluorescent components in DOM and two metals. Triplicate titration experiments showed good reproducibility when assessing the interactions between humic-like components with Cu(ll). Our data show clear differences in metal-DOM interaction for samples of different DOM composition and between two different metals. The results demonstrate that the combination of fluorescence quenching titrations with EEM-PARAFAC was reproducible and sensitive to determine the binding properties of humic-like components with trace metals. The enhancement in fluorescence intensity after its initial decrease for the protein-like components with addition of Cu(II) was observed at mangrove-dominated sites, suggesting changes in the molecular environments of protein-like components due to increased Cu(II) interaction. The application of EEM-PARAFAC in fluorescence quenching studies is a useful tool to evaluate intermolecular DOM and DOM-trace metals interactions.