Clay minerals are prevalent in rock discontinuities and have significant effects on mechanical, hydraulic and seismic properties of rock masses. Understanding seismic behaviours across individual clay-rich rock joints is of great importance in the fields of geology and earth sciences. However, the wave responses of individual clay-rich rock joints have not been well understood until now. This paper reports a laboratory investigation of ultrasonic S-wave propagation and attenuation across single rock joints filled with bentonite clays with varying degree of water saturation. In this study, a series of acoustic measurements were conducted on specimens of the bentonite clay-filled rock joint using a self-developed ultrasonic pulse-transmission test system that equipped with a S-wave transducer pair with a dominant frequency of 250 kHz. Based on the obtained laboratory data, the wave velocity, transmission ratio and the time-frequency-energy distribution of the S-waves transmitted through the bentonite clay-filled joint were calculated and evaluated. The experimental results show that the degree of water saturation of the bentonite clay greatly affects S-wave responses of the filled rock joint. In particular, an increase in the degree of saturation causes a nonlinear decrease in S-wave velocity. In addition, as the water saturation of the bentonite clay increases, the wave attenuation decreases; the minimum wave attenuation is reached at a saturation degree of 71.4% and then the attenuation increases slightly. Additionally, with the increase of the water saturation, the magnitudes of the S-wave energy transmitted across the bentonite clay-filled joint firstly increases and then decreases. The S-wave energy is mostly stored in the frequency range of 150 - 300 kHz regardless of the degree of water saturation of the bentonite clay. This finding indicates that the frequency partition of the transmitted S-waves rarely changes with the changing water saturation. The present work could not only compensate for the lack of laboratory-based research on wave behaviours across clay-rich rock joints but also provides insights into the interpretation of acoustic data from field tests for detecting, characterizing and monitoring rock discontinuities.