Two ca 8000 year long sediment cores from the Gotland Deep, the central sub-basin of the Baltic Sea, were studied by means of digital images, X-radiographs and scanning electron microscopy–energy-dispersive X-ray mineralogical analysis to gain understanding of the physicochemical and biological influences on sedimentary-fabric formation in modern and ancient seas with a high flux of organic carbon, and associated oxygen stress and depauperate ichnofauna. Four lithofacies were recognized: (i) sharply laminated mud; (ii) biodeformed mud; (iii) burrow-mottled mud; and (iv) sedimentation-event bed. The sharply laminated and burrow-mottled facies dominate the cores as alternating long intervals, whereas the biodeformed and sedimentation-event facies occur as thin interbeds within the sharply laminated intervals. The sharply laminated mud comprises alternating diatom-rich and lithic laminae, with occasional Mn-carbonate laminae. Lamination discontinuity horizons within the laminites, where the regular lamination is overlain sharply by gently inclined lamination, challenge the traditional view of mud accumulation by settling from suspension, but indicate localized accumulation by particle-trapping microbial mats and, potentially, by the rapid lateral accretion of mud from bedload transport. The biodeformed interbeds record brief (few years to few decades) oxic–dysoxic conditions that punctuated the anoxic background conditions and permitted sediment-surface grazing and feeding by a very immature benthic community restricted to the surface mixed tier. The likely biodeformers were meiofauna and nectobenthic pioneers passively imported with currents. The sedimentation-event interbeds are distal mud turbidites deposited from turbidity currents probably triggered by severe storms on the adjacent coastal areas. The turbidite preservation was favoured by the anoxic background conditions. The long burrow-mottled intervals are characterized by intensely bioturbated fabrics with discrete Planolites, rare Arenicolites/Polykladichnus and very rare Lockeia trace fossils, as well as bivalve biodeformational structures which represent shallowly penetrating endobenthic feeding and grazing strategies and permanent dwellings. These burrowed intervals represent longer periods (several years to few centuries) of oxic–dysoxic conditions that permitted maturation in the benthos by means of larval settling of opportunistic worm-like macrofauna and bivalves, resulting in the development of a transition tier. These observations imply more dynamic and oxic depositional conditions in Gotland Deep than previously thought. Comparison to previous zoobenthic studies in the area allowed discussion of the benthic dynamics, and the identification of probable biodeforming and trace-producing species. Implications for current biofacies and trace-fossil models are discussed.