The deep waters of the Bransfield Strait receive considerable amounts of water from the Weddell Sea continental shelf. The restricted connections to the surrounding ocean and relatively easier access makes the Bransfield Strait an important proxy region for monitoring changes in the dense Weddell Sea shelf water masses, which are an important precursor of Antarctic Bottom Water (AABW). Long-term hydrographic data from the period 1960s–2010s showed freshening and lightening of the deep water masses of the Bransfield Strait, which was likely caused by large freshwater inputs originating from the western shelf of the Weddell Sea. The rates of freshening and lightening were −0.0010 ± 0.0005 yr−1 and −0.0016 ± 0.0014 kg m−3 yr−1 for the central basin, respectively, and −0.0010 ± 0.0006 yr−1 and −0.0029 ± 0.0013 kg m−3 yr−1 for the eastern basin, respectively. The deep waters showed a high degree of interannual thermohaline variability, which appeared to be caused by changes in the proportions of source water mass mixing between the years. Statistically significant negative correlations between salinity/neutral density fields and the Southern Annular Mode (SAM) were observed (−0.56 and −0.62 for the central basin, respectively, and −0.58 and −0.68 for the eastern basin, respectively) between 1980 and 2014. During SAM positive phases, communication between the Weddell Sea and the Bransfield Strait is reduced, which leads to less saline and lighter water masses in the Bransfield Strait; however, the opposite trends are observed during SAM negative phases.