Although microalgae are recognised to release external organic matter (EOM), little is known about this phenomenon in microalgae cultivation systems, especially on a large scale. A study on the effect of microalgae-stressing factors such as temperature, nutrient limitation and ammonium oxidising bacteria (AOB) competition in EOM production by microalgae was carried out. The results showed non-statistically significant differences in EOM production at constant temperatures of 25, 30 and 35 °C. However, when the temperature was raised from 25 to 35 °C for 4 h a day, polysaccharide production increased significantly, indicating microalgae stress. Nutrient limitation also seemed to increase EOM production. No significant differences were found in EOM production under lab conditions when the microalgae competed with AOB for ammonium uptake. However, when the EOM concentration was monitored during continuous outdoor operation of a membrane photobioreactor (MPBR) plant, nitrifying bacteria activity was likely to be responsible for the increase in EOM concentration in the culture. Other factors such as high temperatures, ammonium-depletion and low light intensities could also have induced cell deterioration and thus have influenced EOM production in the outdoor MPBR plant. Membrane fouling seemed to depend on the biomass concentration of the culture. However, under the operating conditions tested, the behaviour of fouling rate with respect to the EOM concentration was different depending on the initial membrane state.