A sequence stratigraphic framework predicts that time averaging and hiatus durations will be long at times of fastest sea-level rise. This prediction does not necessarily apply to environments where carbonate production keeps up with sea-level rise and where undetected hiatuses decouple short-term from long-term sedimentation rates. The taphonomic clock, however, which measures the residence time of skeletal particles in the mixed layer, can estimate the duration of hiatuses if the rate of skeletal alteration is slow and if skeletal particles endure long-term exposure in the mixed layer. Here, time averaging is calibrated by using evidence from alteration of bivalves in a metrescale Holocene sequence in the Adriatic Sea. In this sequence, transgressive molluscan lags, a maximum-flooding zone shell bed with bivalves, and highstand bryomol assemblages were all deposited under similar long-term sedimentation rates (ca 0.01 to 0.03 cm year À1 ) and exhibit millennial time averaging. Median ages of valves stained by pyrite and cemented by highmagnesium calcitic micritic envelopes exceeding ca 1000 years indicate that: (i) these authigenic processes are slow in subsurface zones with reducing conditions (with prolonged sulphate reduction and carbonate ions sourced from dissolved shells in the surface zones); and (ii) subsurface micrite precipitation prolongs the disintegration half-lives of valves exhumed to surface zones from decades to millennia. The high abundance of stained valves, valves with micrite envelopes, and valves with composite alteration (encrusters and borers colonizing stained and cemented grains) thus identifies hiatuses and skeletal concentrations time-averaged to >1000 years. The upcore decrease in abundance of valves with composite alteration, coupled with temporally-constant long-term sedimentation rates and time averaging, indicates that a temporal decline in sediment exhumation was compensated by a decline in burial of skeletal carbonate produced by molluscs.