Hydroxylated glycerol dibiphytanyl glycerol tetraethers (OH-GDGTs) produced by both marine and freshwater thaumarchaea are increasingly used for the reconstruction of past sea surface temperature (SST). They occur throughout the modern Baltic Sea, but it is unknown if OH-GDGTs can be used for assessing past SST in this area, where salinity has changed considerably over the Holocene. Three commonly applied OH-GDGT proxies for SST reconstruction, i.e., the OH-GDGT%, RI-OH, and RI-OH^′ indices, were tested using a thaumarchaeotal culture enriched from the Baltic Sea grown at 4 and 22 ^∘C, as well as 12 surface sediments from the Baltic Sea and the adjacent Skagerrak. In the culture experiments all three proxies showed the expected response with the rise in temperature, but their absolute values were not always in line with existing marine core-top calibrations, especially for the OH-GDGT% index. Of the two proxies based on the distribution of OH-GDGTs, the RI-OH index shows no increase with increasing mean annual SST, whilst the RI-OH^′ index shows only a linear correlation with SST when the sediments from the Bothnian Sea and Bothnian Bay area, with a reduced salinity and increased lateral sediment influx, are omitted from the dataset. Two sedimentary Holocene records from the Arkona and Gotland basins were studied, the latter in high resolution. In the brackish phase of the Baltic Sea (the Littorina Sea stage), the RI-OH^′ index shows a good correlation with the TEX, an established temperature proxy in the Baltic Sea, and can be used to identify important climatic events. However, during the preceding Ancylus Lake phase the RI-OH^′ (and RI-OH) index records values that are far too high, resulting in anomalously high SST estimates. This is probably because freshwater thaumarchaea adjust their OH-GDGTs differently, as has been shown for thaumarchaea in Lake Lugano's water column. In the Littorina Sea, Ancylus Lake, and Yoldia Lake phases of the Baltic basin, the record of the RI-OH^′ index thus most likely reflects changes in both temperature and salinity. Overall, our study indicates that a reduced salinity increases the values of the RI-OH^′ (and RI-OH) indices substantially, and this should be considered when applying these proxies in other settings.