In this study we investigated and quantified the effects of a number of environmental conditions on the readings of fluorescent dissolved organic matter (fDOM) and total algae probes. These currently monitor fDOM, chlorophyll-a and phycocyanin for the full depth profile of different reservoirs in South-East Queensland (Australia), but interferences and quenching affecting these parameters have led to uncertainty in the reliability of the readings. Additionally, in the case of the total algae probe, obtaining reliable estimates of algal biovolume or cell counts is challenging since the pigments content varies with species and several other environmental variables influence estimates. With regards to the fDOM, a number of experiments were performed which enabled the development of a sequential compensation model accounting for the main trivial quenching. In addition, the compensated readings were compared to other experiments’ outputs to check for correlations between readings and character/molecular weight of DOM to develop an accurate real-time model that may be useful in assisting DOM removal by coagulation. Preliminary work with the algae probe also showed potential to derive more specific information on species/abundance for better cyanobacteria management.