Abstract. Although the depth of bioturbation can be estimated on the basis of ichnofabric, the timescale of sediment mixing (reworking) and irrigation (ventilation) by burrowers that affects carbonate preservation and biogeochemical cycles is difficult to estimate in the stratigraphic record. However, pyrite linings on the interior of shells can be a signature of slow and shallow irrigation. They indicate that shells of molluscs initially inhabiting oxic sediment pockets were immediately and permanently sequestered in reduced, iron-rich microenvironments within the mixed layer. Molluscan biomass-stimulated sulfate reduction and pyrite precipitation was confined to the location of decay under such conditions. A high abundance of pyrite-lined shells in the stratigraphic record can thus be diagnostic of limited exposure of organic tissues to O2 even when the seafloor is inhabited by abundant infauna disrupting and age-homogenizing sedimentary fabric as in the present-day northern Adriatic Sea. Here, we reconstruct this sequestration pathway characterized by slow irrigation (1) by assessing preservation and postmortem ages of pyrite-lined shells of the shallow-infaunal and hypoxia-tolerant bivalve Varicorbula gibba in sediment cores and (2) by evaluating whether an independently documented decline in the depth of mixing, driven by high frequency of seasonal hypoxia during the 20th century, affected the frequency of pyrite-lined shells in the stratigraphic record of the northern Adriatic Sea. First, at prodelta sites with a high sedimentation rate, linings of pyrite framboids form rapidly in the upper 5–10 cm as they already appear in the interiors of shells younger than 10 years and occur preferentially in well-preserved and articulated shells with periostracum. Second, increments deposited in the early 20th century contain < 20 % of shells lined with pyrite at the Po prodelta and 30 %–40 % at the Isonzo prodelta, whereas the late 20th century increments possess 50 %–80 % of shells lined with pyrite at both locations. At sites with slow sedimentation rate, the frequency of pyrite linings is low (< 10 %–20 %). Surface sediments remained well mixed by deposit and detritus feeders even in the late 20th century, thus maintaining the suboxic zone with dissolved iron. The upcore increase in the frequency of pyrite-lined shells thus indicates that the oxycline depth was reduced and bioirrigation rates declined during the 20th century. We hypothesize that the permanent preservation of pyrite linings within the shells of V. gibba in the subsurface stratigraphic record was enabled by slow recovery of infaunal communities from seasonal hypoxic events, leading to the dominance of surficial sediment modifiers with low irrigation potential. The presence of very young and well-preserved pyrite-lined valves in the uppermost zones of the mixed layer indicates that rapid obrution by episodic sediment deposition is not needed for preservation of pyrite linings when sediment irrigation is transient and background sedimentation rates are not low (here, exceeding ∼ 0.1 cm yr−1) and infaunal organisms die at their living position within the sediment. Abundance of well-preserved shells lined by pyrite exceeding ∼ 10 % per assemblage in apparently well-mixed sediments in the deep-time stratigraphic record can be an indicator of inefficient bioirrigation. Fine-grained prodelta sediments in the northern Adriatic Sea deposited since the mid-20th century, with high preservation potential of reduced microenvironments formed within a mixed layer, can represent taphonomic and early diagenetic analogues of deep-time skeletal assemblages with pyrite linings.