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The Baltic Sea, a dynamic, marginal marine basin, experienced a number of large changes in salinity during the Holocene as a result of fluctuations in global and local sea level related to melting of glacial ice sheets and subsequent isostatic rebound. These changes likely had pronounced effects on the species composition of haptophytes, a common phytoplankton group found in the Baltic Sea. This dynamic environment provides the ideal setting to study how species change impacts distribution and hydrogen isotope ratios of long‐chain alkenones (δ2HC37), haptophyte‐specific biomarkers. Here we analyzed the aforementioned parameters in Holocene sediments covering the contrasting hydrological phases of the Baltic Sea. Alkenone distributions changed with different Baltic Sea salinity phases, suggesting that species shifts coincide with salinity change. δ2HC37 values show two major shifts: one in the middle of the freshwater Ancylus Lake phase (10.6 to 7.7 ka) and a second at the transition from the brackish Littorina Sea phase (7.2 to 3 ka) into the fresher Modern Baltic (3 ka to the present). The first shift represents a significant enrichment of 50‰, which cannot be explained by salinity or species changes only. At this time, the isotopically depleted ice sheets had melted, and only the relatively enriched freshwater source remained. The second shift, coincident with a change in distribution, is likely caused by a change in species composition alone. These findings show that hydrogen isotope ratios of long‐chain alkenones, combined with their relative distribution, can be used to reconstruct changes in source water.