Data from cruises between 1989 and 2003 with FS Polarstern were used to construct section-wide potential temperature and salinity time series of the main water masses in the Weddell Gyre. In tandem with these CTD data, two time series between 1989 and 1995 are presented from moored instruments in the central Weddell Sea. The regional and methodological consistency of the data set allows us to quantify variations which are not visible in less homogeneous data sets. The data reveal significant temperature and salinity variations of the Warm Deep Water and the Weddell Sea Bottom Water on a decadal time scale. The longest time series were obtained at the prime meridian. Here warming is observed in the Warm Deep Water from 1992 to 1998 followed by cooling. In the Weddell Sea proper, measurements of instruments moored in the Weddell Sea Bottom Water layer recorded a temperature increase over 6 years at a rate of 0.01°C yr-1. After the mooring period, CTD casts in 1998 point to a weakening of the trend. The warming trend in the bottom water occurs over most of the Weddell Sea as detected in the additional CTD surveys. The variations are close to the detection level in the voluminous Weddell Sea Deep Water. The initial warming trend of the Warm Deep Water is consistent with warming trends reported in literature of subsurface waters of the Antarctic Circumpolar Current. The reversal of the trend in the Weddell Sea seems to be related to variations of the atmospheric conditions which can affect both the intrusion of Circumpolar Deep Water from the north and the circulation of the Weddell Gyre. Because the Warm Deep Water is the major source water for the formation of deep and bottom water in the Weddell Sea, it is suggested that its increase of temperature and salinity is likely to at least partly cause the variations which were observed in the bottom water.