Abstract. Although the depth of bioturbation can be estimated on the basis of ichnofabric, the time scale of sediment mixing and irrigation by burrowers that affects carbonate preservation and biogeochemical cycles is difficult to estimate in the stratigraphic record. However, pyrite linings on interior of shells can be a signature of slow mixing and irrigation rate because they indicate that shells of molluscs initially inhabiting oxic sediment zones were immediately and permanently sequestered in reduced microenvironments where molluscan biomass and associated microbial coatings stimulated sulfate reduction and pyrite precipitation. A high abundance of pyrite-lined shells in the stratigraphic record can thus be diagnostic of limited net exposure of labile tissues to O2 even when the seafloor is inhabited by abundant burrowing infauna as in the present-day northern Adriatic Sea. Here, we reconstruct this sequestration pathway (1) by assessing preservation and postmortem ages of pyrite-lined shells of the hypoxia-tolerant bivalve Varicorbula gibba in sediment cores and (2) by evaluating whether an independently-documented decline in bioturbation, driven by eutrophication and 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 high sedimentation rate, linings of pyrite framboids form rapidly in near-surface sediment zones as they appear already in interiors of shells and in intra-shell conchiolin layers younger than 10 years and occur preferentially in well-preserved and articulated shells with periostracum and relatively high concentrations of amino acids. Second, increments deposited in the early 20th century contain < 20 % of shells with pyrite at the Po prodelta and 30–40 % at the Isonzo prodelta, whereas the late 20th century increments possess 50–80 % of shells with pyrite at both locations. At sites with slow sedimentation rate, the frequency of pyrite linings is low (< 10–20 %). Third, the upcore increase in the frequency of pyrite-lined shells positively correlates with an abrupt increase in maximum shell size and biomass of V. gibba. Therefore, the upcore increase in the frequency of pyrite-lined shells indicates that sediment mixing and bioirrigation rates declined during the 20th century, leading to higher sequestration of pyrite-lined shells during the late 20th century. We hypothesize that the permanent preservation of pyrite linings within the shells of V. gibba in the subsurface stratigraphic record was allowed by slow recovery of infaunal communities frequently interrupted by seasonal hypoxic events, leading to the dominance of surficial sediment modifiers with low irrigation potential. 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 short net exposure of shells to O2 and inefficient bioirrigation. Fine-grained prodelta sediments in the northern Adriatic Sea deposited since the mid-20th century, with high preservation potential of reduced microniches, can represent taphonomic and early-diagenetic analogues of deep-time skeletal assemblages with pyrite linings.