Physical, microstructural, hydraulic and mechanical properties of Ypresian clays were investigated by identification tests, SEM, MIP and oedometer tests on the samples taken from a borehole at Kallo at 290–400 m depth. The results showed that Ypresian clays are highly plastic and of relatively low density with high swelling clay content. Their physical, mineralogical properties present significant variations over depth. Two microstructural arrangements, matrix-type with higher and aggregate-type with lower swelling content, were identified. The former exhibits bi-modal porosity while the latter shows mono-modal porosity but with a larger dominant pore size. The permeability with matrix-type microstructure is significantly lower than that with aggregate-type despite their higher void ratio. These microstructural features result in the initial unsaturated state of the samples. Hysteretic unloading–reloading loops, explained by a microstructure-based swelling stress concept, are identified on oedometer tests. The variation of this swelling stress with the corresponding initial void ratio over depth perfectly reflects the physical variations and is consistent with that determined from common swelling tests. The yield stress ratios are slightly higher than the over-consolidation ratio, suggesting negligible effects of diagenesis, etc. The variations of compression and swelling slopes are consistent with the physical and microstructural variations.