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Although many studies assessed fouling behaviour in microporous membrane processes like membrane bioreactors (MBRs), in situ or direct observation of the fouling layer has not yet been possible. The observation of the fouling layer resulting from the filtration of model solutions allowed better understanding of MBR fouling intensity and mechanisms. In this study, alginate has been used as a model for polysaccharide (one of the main foulants in MBRs). Three visualisation techniques, confocal laser scanning microscopy (CLSM), environmental scanning electron microscopy (ESEM), and direct observation (DO) have been tested to observe the alginate fouling. The work presented in this paper revealed the advantages and limitations of each technique used for this specific application. Although no coating is required for this technique, ESEM allowed distinct non-destructive observation of clean membrane. However, the lack of structure in the alginate fouling layer limited the use of this technique for fouled membranes. While CLSM requires the use of expensive fluorescent markers, DO appeared as the most promising technique for direct and in situ observation of MBR fouling. DO of alginate/bentonite and alginate/bacteria solutions revealed the creation of a well-structured dual fouling system (bentonite-concentrated layer of 50 μm embedded and covered by a concentration polarisation of alginate greater than 240 μm) on the surface of hollow fibre membrane.