In Activated Sludge (AS) process, the impact of the operational parameters on process efficiency is presumably correlated to the sludge properties. This study provides a better insight of this conjoint interaction by subjecting a lab-scale AS system to a sequence of operating condition modifications enabling typical situations of a wastewater treatment plant to be represented. Process performance was assessed and AS floc morphology (size, circularity, convexity, solidity and aspect ratio) was quantified measuring 100,000 flocs per sample with an automated image analysis technique. Introducing 3D-distributions, which combine morphological properties, allows the identification of a filamentous bulking characterized by a floc population shift towards larger sizes and lower solidity and circularity values. Moreover, a washout phenomenon was characterized by smaller AS flocs and an increase in their solidity. Recycle ratio increase and COD:N ratio decrease both promoted a slight reduction of floc sizes and a constant evolution of circularity and convexity values. The analysis of the volume-based 3D-distributions turned out to be a smart tool to cross size and shape data allowing a deepest understanding of the dynamics of floc structure under process disturbances.