Abstract In this study, a two-site fluorescence quenching data treatment was developed based on the Ryan–Weber model to investigate natural organic matter complexation with uranyl ion. Parameters for each ligand site including stability constant (log K ), ligand site concentration ( C L ) and residual fluorescence intensity ( I res ) were determined using this approach. Parallel factor (PARAFAC) analysis was used to obtain quantitative data for peaks from fluorescence excitation emission matrix (EEM) spectra. This model was tested using a Cu 2 + titration with a mixed system of tyrosine and tryptophan to simulate two ligands. Relatively good agreements with literature values (within 3.29% for log K values) indicated the validity of the model. The model was further applied in the complexation study between soil fulvic acid (SFA) and UO 2 2 + since two components were predicted using core consistency diagnoses (CORCONDIA) for our SFA sample. Results for 20 mg/L SFA at pH 3.50 for the peak at λ ex = 330 nm, λ em = 450 nm were log K = 4.49, C L = 5.05 μmol/L, and I res = 15.1 and for the peak at λ ex = 240 nm, λ em = 450 nm were log K = 4.56, C L = 4.56 μmol/L, and I res = 1.2.