The variations in the Baltic Sea salinity and the mean halocline depth during 1961-2007 are studied using Rossby Centre Ocean model. The largest trend in the monthly mean salinity averaged over the top 15 m was found in the Gulf of Riga and Baltic proper, while the trend in the northernmost part was non-existant. A period with shallow halocline in the Baltic Sea during 1970-1975 was identified and a period with deep halocline during 1990-1995 with the difference exceeding more than 15 m in the Baltic proper between the two time-periods. Model simulation indicated that the mean surface salinity in the Baltic Sea is spatially controlled by the accumulated river runoff, while the mean salinity below the halocline in the Baltic proper by the mean zonal and absolute wind speed. The halocline depth in the Baltic Sea is affected significantly by the freshwater content and absolute wind speed. The impact of the mean zonal wind speed to the mean halocline depth in the Baltic proper is moderate, while the impact of runoff is low.