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Rock joints in faulted zones are usually filled with large amounts of fault gouge, in which clay-rich fillings are very common. Fault water can significantly influence the mechanical parameters of clay-rich fillings and affect the shear mechanical behaviour of rock joints. Based on a tunnelling project passing through a faulted zone in Yunnan Province of China, this paper investigates the mechanical behaviour of rock joints with clay-rich fillings. A series of direct shear tests are conducted on rock joint samples made from rock blocks and fillings collected from a fault zone. The shear stress‒displacement curves and shear failure characteristics of rock joints are obtained, and several key factors of the fillings are considered, such as particle size, mineral composition, clay content, and water content. Furthermore, the peak and residual shear strengths are analysed by considering the influence of the water content and normal loading pressure. The test results show that water content of fillings has a great influence on shear strength of clay-filling rock joints; there is a trend to a negative correlation between the shear strength of rock joints when water content (w) exceeds the plastic limit (wp). Finally, a shear strength model for rock joints with clay-rich fillings is proposed based on the JRC-JCS strength criterion. Influence of water content on the shear strength of rock joints with clay-rich fillings is studied. A series of direct shear tests are conducted on rock joint samples based on a tunnelling project. The shear stress–displacement curves of rock joints with clay-rich filling are obtained. A shear strength weakening model of clay-filled joints is proposed. Highlights: Influence of water content on the shear strength of rock joints with clay-rich fillings is studied. A series of direct shear tests are conducted on rock joint samples based on a tunnelling project. The shear stress-displacement curves of rock joints with clay-rich filling are obtained. A shear strength weakening model of clay-filled joints is proposed. [ABSTRACT FROM AUTHOR]