Removing dissolved organic matter (DOM) from the source water is critical for the drinking water treatment process. The low molecular weight hydrophilic fraction of DOM is generally recalcitrant to removal by coagulation, and the DOM bypassing the coagulation/filtration stages of treatment will likely react with the disinfecting agent at the end of the treatment process, leading to the formation of potentially carcinogenic disinfection by products (DBPs) such as trihalomethanes (THMs). Each specific fraction of DOM reacts with a particular disinfecting agent to form different DBPs; some with higher toxicity and carcinogenicity than others. Understanding the DBPs formation pathways, however, is a difficult task since DOM present in the source water are likely to be highly degraded compounds that differ from each other, forming a mixture of diverse molecules which are extremely challenging to individually characterise. Hence, there is a need for monitoring certain fractions of DOM, such as humic acids, by tracking down DOM characteristics and concentration levels in source waters. DOM characterisation techniques can be divided into three groups. The first group investigates the abundance and nature of structural units, providing detailed structural information. The second group looks into the chemical behaviour of DOM, its molecular weight, molecular size, distribution, and hydrophobicity-hydrophilicity. It also focuses on its polymeric nature and ability to provide good molecular separation. The third group measures the fluorescence signal of DOM in situ, without directly scrutinising chemical identities of functional groups or molecules. However, the methods used in the first two groups are complicated and time-intensive, making them unsuitable for remote online monitoring of DOM characteristics. In contrast, the currently available fluorescence probes provide a simple, sensitive, rapid, non-invasive way of in-situ estimation of the fluorescent DOM (fDOM). Despite the potential beneficial applications of this relatively new technology, field fDOM measurements are subject to interferences caused by changes in temperature, turbidity, pH, salinity and inner filter effect (IFE). This often makes probe readings unreliable; as a result, they are rarely used by water treatment plant operators. Thus, accurate and reliable compensation models should be designed and applied to raw fDOM readings collected by fluorescence probes, in order to make them a useful decision support tool for water treatment plant operators. 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 IFE. The compensation model was developed and validated for an Australian subtropical reservoir. Three other Australian reservoirs were also investigated to investigate the role that particle size distribution plays on light scattering, and molecular weight links to fDOM signal intensity. Findings revealed that quenching due to turbidity and IFE effects was 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 fDOM readings had a high correlation with the low (< 500Da) molecular weight fraction of the DOM, which is more recalcitrant to removal by coagulation. As a consequence there is potential to use fDOM probes to provide real-time, in-situ information on DOM properties in freshwater systems, which will enable water treatment plants operators to optimise the coagulation process.