Global climate change is driving widespread transformations in the ocean. The South Atlantic, a key component of the global meridional overturning circulation that regulates the climate, is thought to be undergoing large-scale and deep-reaching compound state changes in temperature and salinity throughout the basin, but the underlying physical processes remain unclear. In this study, leveraging advanced ocean observing networks, we investigate the observational evidence and the physical processes shaping both individual and compound (temperature–salinity coupled) changes from a water-mass perspective based on rigorous analyses of observational uncertainty. We find that there are substantial properties changes in all upper-ocean water masses in the South Atlantic over the past 45 years, in which the physical contributions of these changes are due to distinct dynamic and thermohaline processes across different water masses: Surface Water has warmed and become saltier since the 1980s, accompanied by a ~10 % increase in volume driven. The South Atlantic Central Water has expanded vertically by ~1.15 times driven by vertical displacement. The Antarctic Intermediate Water has warmed by roughly 0.25 °C, leading to a density decrease dominated by thermal effects. The pronounced intermediate water warming signal represents a potential early fingerprint of anthropogenic change, now affecting ~70 % of the basin. It has been mixed and advected near-isopycnally into the South Atlantic from the Subpolar Front, Southern Ocean and the Indian Ocean. This study advances basin-scale observational evidences and the physical mechanisms underlying regional individual and compound changes, providing new insight into regional climate variability and long-term changes in a warming climate.