The Agulhas Current, like all western boundary currents, transports salt from the subtropics toward the poles and, on average, acts as a barrier to exchange between the open ocean and the continental seas. Uniquely, the Agulhas jet also feeds a leakage of relatively salty waters from the Indian into the Atlantic Ocean. Despite its significance, the signals and drivers of water mass variability within the Agulhas Current are not well known. To bridge this gap we use 26 months of moored observations to determine how and why salinity – a water mass tracer – varies across the Agulhas Current. We find that salinity variability is driven by both shifting (i.e. changes in location) and pulsing (i.e. changes in strength) of the current. Shifting of the current causes heave and diapycnal mixing of subtropical, central, and intermediate waters. Diapycnal mixing between central and intermediate waters explains most of the variability, creating salinity anomalies between -0.4 and +0.1 psu. Pulsing of the current drives heave and, to a lesser extent, along-isopycnal mixing within the halocline. This cross-stream mixing results in salinity anomalies of up to 0.3 psu. The mean and standard deviation of Agulhas Current volume and salt transports are -76 and 22 Sv and -2650 and 770 Sv psu. Transport weighted salinity has a standard deviation of 0.05 psu. We estimate that O(1013) kg yr−1 of the salt transported southwestward leaks into the fresher Atlantic Ocean. Based on our observations, the variability of the Agulhas Current could alter this salt leakage by an order of magnitude.