This work investigates the impact of regional climatic changes upon the salinity field of Todos os Santos Bay (BTS), the third largest estuary in the country. A comprehensive meteorological and oceanographic data set was used, which included more than 50 years of rainfall, river discharge and air temperature, 7 years of hydrodynamic numerical simulations of the bay and adjacent shelf, and 3 years of observations of the salinity field. The results show a clear aridification (less humidity and warmer air temperatures) trend in the last 5-6 decades. In this period, the yearly mean fluvial discharges and total rainfall were reduced by up to 72% and 50%, respectively, of their climatological means, and the air temperature increased by up to 1.25 °C. Less freshwater inflow and higher temperatures caused an increase of the mean surface salinity of 0.6 for the whole bay and 1.2 in the most internal sectors. Hypersalinity events apparently occurred for the first time in the early 1990s, and reached a maximum intensity in 2013 during the worst regional draught in the historical record, when an estuarine density plug was observed. The hypersalinity events were intensified, and not caused by the damming of Paraguaçu River, whose summer discharges have decreased faster than anticipated by previous investigations. The original tropical climate of the region has become more Mediterranean, with relatively less rainfall occurring in the summer. The hydrographic changes of the BTS exemplify similar hydrological and hydrographic processes that might also be underway in tropical areas undergoing climate aridification.