Fluorescence excitation–emission matrix (EEM) spectroscopy is often used to determine the levels of trihalomethane (THM) precursors in natural organic matter. However, humic substances are known to quench the fluorescence of amino acids and proteins. To date, none of the EEM-based models for predicting THM formation potential (THMFP) have explicitly accounted for these quenching effects. Thus, we investigated the importance of correcting for fluorescence quenching during THMFP prediction. Fluorescence titration experiments revealed that the correction improved the accuracy of THM prediction. EEM-based models using the corrected fluorescence intensity displayed the highest accuracy (R2 > 0.99; mean absolute error 8.1 μg/L and 13.9 μg/L for chloroform and bromoform, respectively) among models using individual parameters of EEM intensity, dissolved organic carbon (DOC), ultraviolet absorbance at 254 nm (UV254), specific UV254 (SUVA254) and differential ultraviolet absorbance at 272 nm (ΔUV272). Thus, EEM-based models require both the fluorescence intensity of a humic-like component and the corrected fluorescence intensity of a protein-like component for accurate THMFP prediction, for both chlorination and bromination processes. We also found it to be unnecessary to combine DOC with EEM intensity in terms of prediction accuracy, as long as the fluorescence quenching correction is applied.