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Abstract Oceanographic and evolutionary inferences based on fossil assemblages can be obscured by age offsets among co‐occurring shells (i.e., time averaging). To identify the contributions of sedimentation, mixing, durability, and production to within‐ and between‐species age offsets, we analyze downcore changes in the age‐frequency distributions of two bivalves on the California shelf. Within‐species age offsets are ~50–2,000 years forParvilucinaand ~2,000–4,000 years forNuculanaand between‐species offsets are 1,000–4,000 years within the 10‐ to 25‐cm‐thick stratigraphic units. Shells within the top 20–24 cm of the seabed are age‐homogeneous, defining the thickness of the surface completely‐mixed layer (SML), and have strongly right‐skewed age‐frequency distributions, indicating fast shell disintegration. The SML thus coincides with the taphonomic active zone and extends below the redoxcline at ~10 cm. Shells >2,000–3,000 years old occurring within the SML have been exhumed from subsurface shell‐rich units rich where disintegration is negligible (sequestration zone, SZ). Burrowers (callianassid shrimps) penetrate 40–50 cm below the seafloor into this SZ. The millennial offsets within each increment result from the advection of old shells from the SZ, combined with an out‐of‐phase change in species production. Age unmixing reveals thatParvilucinawas abundant during the transgressive phase, rare during the highstand phase, and increased steeply in the twentieth century in response to wastewater.Nuculanawas abundant during the highstand phase and has declined over the past two centuries. This sequestration‐exhumation dynamic accentuates age offsets by allowing both the persistence of shells below the SML and their later admixing with younger shells within the SML.