The identification of key foulants and the provision of early warning of high fouling events for drinking water treatment membrane processes is crucial for the development of effective countermeasures to membrane fouling, such as pretreatment. Principal foulants include organic, colloidal and particulate matter present in the membrane feed water. In this research, principal component analysis (PCA) of fluorescence excitation-emission matrices (EEMs) was identified as a viable tool for monitoring the performance of pre-treatment stages (in this case biological filtration), as well as ultrafiltration (UF) and nanofiltration (NF) membrane systems. In addition, fluorescence EEM-based principal component (PC) score plots, generated using the fluorescence EEMs obtained after just 1hour of UF or NF operation, could be related to high fouling events likely caused by elevated levels of particulate/colloid-like material in the biofilter effluents. The fluorescence EEM-based PCA approach presented here is sensitive enough to be used at low organic carbon levels and has potential as an early detection method to identify high fouling events, allowing appropriate operational countermeasures to be taken.