This work deals with the development of a digital image analysis procedure to characterize microbial flocs obtained in three different WWTP: a bench-scale Sequencing Batch Reactor (SBR) dealing with phenol and nitrogen biological removal, a municipal treatment unit (Ilha do Governador, Rio de Janeiro, Brazil) and an industrial wastewater treatment plant (Ciba – Estrada do Colégio, Rio de Janeiro, Brazil). The developed procedure permits to obtain its morphological parameters like equivalent diameter, compactness, roundness and porosity properties as well as the fractal dimension. This procedure was validated and lead to identify the major relationships between the analysed morphological parameters. A minimum of 300 flocs should be included in the image analysis and a significant influence of the sample dilution step on the mean size of the flocs was verified. The porosity parameter positively correlated with the fractal dimension of microbial aggregates indicating the that highly porous flocs are very irregular.