This study explores the Holocene depositional succession at the IODP Expedition 347 sites M0061 and M0062 in the vicinity of the Ångermanälven River estuary in the Bothnian Sea sector of the Baltic Sea in northern Scandinavia. Site M0061 is located in a coastal offshore setting (87.9 m water depth), whereas site M0062 is fully estuarine (69.3 m water depth). The dataset comprises acoustic profiles and sediment cores collected in 2007 and late 2013 respectively. Three acoustic units (AUs) were recognized. Lowermost AU1 is interpreted as a poorly to discontinuous stratified glaciofluvial deposit, AU2 as a stratified conformable drape of glaciolacustrine origin, and AU3 as a poorly stratified to stratified mud drift. A strong truncating reflector separates AU2 and AU3. Three lithological units (LUs) were defined in the sediment cores. LU1 consists of glaciofluvial sand and silt gradating into LU2, which consists of glaciolacustrine varves. A sharp contact interpreted as a major unconformity separates LU2 from the overlying LU3 (brackish-water mud). In the basal part of LU3, one debrite (site M0061) or two debrites (site M0062) were recognized. Information yielded from sediment physical properties (magnetic susceptibility, natural gamma ray, dry bulk density), geochemistry (total carbon, total organic carbon, total inorganic carbon and nitrogen), and grain size support the LU division. The depositional succession was formally subdivided into two alloformations: the Utansjö Alloformation and overlying Hemsön Alloformation; the Utansjö Alloformation was further subdivided into two lithostratigraphic formations: the Storfjärden and Åbordsön formations. The Storfjärden (sandy outwash) and Åbordsön (glaciolacustrine rhythmite) formations represent a glacial retreat systems tract, which started at ca. 10.6 kyr BP. Their deposition was mainly controlled by meltwater from the retreating ice margin, glacio-isostatic land uplift and the regressive (glacial) lake level. The Hemsön Alloformation (organic-rich brackish-water mud) represents a period of forced regression, starting possibly at ca. 9.5 kyr BP. At about 7 kyr BP, brackish water reached the study area as a result of the mid-Holocene marine flooding of the Baltic Sea Basin, but the rapid land uplift soon surpassed the associated (Littorina) transgression. Changed near-bottom current patterns, caused by the establishment of a permanent halocline, and the reduced sediment consistency caused by increased organic deposition resulted in a sharp and erosional base of the brackish-water mud. Estuarine processes and salinity stratification at site M0062 started to play a more important role. This study applies a combined allostratigraphic and lithostratigraphic approach over the conventional Baltic Sea stages. This approach makes it more straightforward to study this Baltic Sea deglaciation–postglacial sequence and compare it to other formerly glaciated shallow sea estuaries.