The large‐scale shifts in the salinity of the Baltic Sea over the Holocene are well understood and have been comprehensively documented using sedimentary proxy records. More recent work has focused on understanding how past salinity fluctuations have affected other ecological parameters (e.g. primary productivity, nutrient content) of the Baltic basin, and salinity changes over key events and over short time scales are still not well understood. The International Ocean Drilling Program Expedition 347 cored the Baltic basin in order to collect basin‐wide environmental records through a glacial–interglacial cycle. Site M0059 is located in the Little Belt between the Baltic Sea and the Atlantic Ocean. A composite splice section from Site M0059 was analysed at a decadal resolution to study changes in salinity, nutrient conditions and other surface water column parameters based on changes in diatom assemblages and on quantitative diatom‐based salinity inferences. A mesotrophic slightly brackish assemblage is seen in the lowermost analysed depths, corresponding to 7800–7500 cal. a BP. An increase in salinity and nutrient content of the water column leads into a meso‐eutrophic brackish phase. The observed salinity increase is rapid, lasting from 7500 to 7150 cal. a BP. Subsequently, the Little Belt becomes oligotrophic and is dominated by tychopelagic diatoms from c. 7100 to c. 3900 cal. a BP. This interval contains some of the highest salinities observed followed by diatom assemblages similar to those of the Northern Atlantic Ocean, composed primarily of cosmopolitan open ocean marine diatoms. A return to tychopelagic productivity is seen from 3850 to 980 cal. a BP. Anthropogenic eutrophication is detected in the last 300 years of the record, which intensifies in the uppermost sediments. These results represent the first decadally resolved record in the region and provide new insight into the transition to a brackish basin and subsequent ecological development.