Late Holocene sediments in the Baltic Sea provide an opportunity to study lateral changes in the assemblages of identifiable biogenic sedimentary structures (ichnofossils) in a large, high-latitude semi-enclosed sea with instrumentally determined gradients in biodiversity and environmental factors such as salinity and oxygen availability. Integrated sedimentological and ichnological analysis is carried out on 6 long cores collected along an open-sea, declining salinity transect across the basin. Muddy sediments in euhaline (Kattegat) and polyhaline (Mecklenburg Bight) sites are characterized by the archetypal Cruziana Ichnofacies, portrayed by subsurface deposit-feeding structures ( Scolicia and Planolites), surface deposit-feeding structures ( Skolithos), and structures that reflect both these feeding strategies ( Palaeophycus, Arenicolites/ Polykladichnus and unnamed biodeformational structures produced by bivalves). The ichnofossils are tiered to 3 levels. The Cruziana Ichnofacies is impoverished in the higher mesohaline Arkona Basin and even more so with declining salinity farther inland. The deepest, oxygen-restricted study sites (Gotland Deep and the western Gulf of Finland) below a permanent halocline are characterized by very small and shallow deposit-feeding structures ( Planolites and rare flat Arenicolites/ Polykladichnus), and poorly developed tiering. The nearly freshwater eastern Gulf of Finland is characterized by the Cenozoic archetypal Mermia Ichnofacies, dominated by narrow and shallow subsurface and surface deposit-feeding structures ( Planolites and flat Arenicolites/ Polykladichnus). Large Planolites (3–7 mm in diameter) at this site are untypical of Mermia Ichnofacies assemblages. These results confirm the earlier observations that marine forms dominate brackish-water ichnoassemblages, with the ichnofossil size and diversity decreasing with declining salinity. The results also confirm the predicted decreases in the ichnofossil size and vertical extent at low-oxygen levels. Poorly developed tiering is a particularly useful indicator of oxygen stress in the salinity-restricted system.