The recent deployment of fluorescent dissolved organic matter (fDOM) probes in dam catchments and drinking water treatment plants (DWTP) for water quality monitoring purposes has resulted in the production of a large amount of data that requires scientific evaluation. This study introduces a comprehensive, transferable methodological framework for scientists and water professionals to model fluorescence site-specific quenching on fDOM probe readings caused by temperature, suspended particles, and the inner filter effect (IFE) and applies it to an Australian subtropical reservoir. The findings revealed that quenching due to turbidity and IFE effects were best predicted by threshold autoregressive models. Raw fDOM probe measurements were validated as being more reliable if they were systematically compensated using the proposed procedure. The developed fDOM compensation procedure must consider the instrument features (i.e., wavelength broadband and responsiveness) and site-specific conditions (i.e., DOM characteristics and suspended particles). A finding of particular interest was that the compensated normalized fDOM readings had a high correlation with the low (<500 Da) molecular weight fraction of the DOM, which is more recalcitrant to removal by coagulation. As a consequence, there is potential to use compensated fDOM probe readings to provide real-time, in situ information on DOM properties in freshwater systems, which will enable water treatment plant operators to optimize the coagulation process.