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This study explores the effect of suppressed surface charges on the sedimentation behaviour and fabric of kaolinite clay. In particular, sedimentation behaviours were compared between negatively charged natural kaolin clays and surface-treated and hence electrically suppressed kaolin clays by methylene blue adsorption. The results clearly indicate that the negative surface charge impeded the sedimentation rate of kaolin by resisting particle aggregation. Such an effect appeared the most significant when the surrounding pH was less than the isoelectric point (IEP) of the mineral edges. Under a pH less than IEP, the flocculation time and the final void ratio remarkably dropped after the negative charge neutralisation. This was also corroborated by the scanning electron microscopy images, which further revealed the fabric transition from an edge-to-face flocculated structure to a face-to-face aggregated structure due to the absence of interparticle electrical forces. Conversely, there was no significant fabric change at pH higher than or near the IEP, even though the sedimentation behaviours were accelerated by forming larger flocs. This study imparts important insights into the fundamentals of microstructure and resulting sedimentation behaviour of clayey soils and how they can be changed in electrically neutralised clay.