Bentonite, a smectite clay, is widely used in geotechnical engineering as drilling mud, liner material, and it has been proposed as buffer and backfill material for high-level nuclear waste disposal. An understanding of the microstructure formation of bentonite and its hydrophobic properties would enable the development of a methodology capable of predicting its behaviour when exposed to water. This study aims to gain an understanding of the microstructure formation of bentonite, specifically Kunigel-VI, by comparing its behaviour with that of a non-swelling clay, NSF Clay. Three different tests were performed to observe this behaviour: Constant Rate of Strain (CRS) consolidation testing, Mercury Intrusion Testing (MIT), and Scanning Electron Microscopy (SEM). Results indicated that aggregate formation occurred in both clays, but at water contents higher than 50 %, the aggregates in NSF Clay collapsed, while those of Kunigel-VI increased in number and size. An increase in applied pressure resulted in the dissipation of air, and a decrease in size of the intra and inter-aggregate spaces.