Optical sensors for fluorescence of chlorophyll a (f-Chl a) and phycocyanin (f-PC) are increasingly used as a proxy for biomass of algae and cyanobacteria, respectively. They provide measurements at high-frequency and modest cost. These sensors require site-specific calibration due to a range of interferences. Light intensity affects the fluorescence yield of cyanobacteria and algae through light harvesting regulation mechanisms, but is often neglected as a potential source of error for in-situ f-Chl a and f-PC measurements. We hypothesised that diel light variations would induce significant f-Chl a and f-PC suppression when compared to dark periods. We tested this hypothesis in a controlled experiment using three commercial fluorescence probes which continuously measured f-Chl a and f-PC from a culture of the cyanobacterium Dolichospermum variabilis as well as f-Chl a from a culture of the green alga Ankistrodesmus gracilis in a simulated natural light regime. Under light, all devices showed a significant (p<0.01) suppression of f-Chl a and f-PC compared to measurements in the dark. f-Chl a decreased by up to 79% and f-PC by up to 59% at maximum irradiance compared to dark-adapted periods. Suppression levels were higher during the second phase of the diel cycle (declining light), indicating that quenching is dependent on previous light exposure. Diel variations in light intensity must be considered as a significant source of bias for fluorescence probes used for algal monitoring. This is of high relevance as most monitoring activities take place during daytime and hence f-Chl a and f-PC are likely to be systematically underestimated under bright conditions. Compensation models, design modifications to fluorometers and sampling design are discussed as suitable alternatives to overcome light-induced fluorescence quenching.