Abstract Presented are the results of studying the variations of thermohaline and hydrochemical characteristics of the Baltic Sea in the second half of the 20th century and in the early 21st century based on the data of shipborne measurements. Trends in temperature, salinity, and hydrochemical parameters are revealed, and their significance is estimated. The quantile analysis is carried out. It is demonstrated that the temperature of the surface and bottom layers rises and the variations of salinity and oxygen content have a significant negative trend. It is revealed that the hypoxic conditions whose periods increase by several times at the absence of major Baltic inflows are formed in the areas of deep trenches.