Shells in modern seabeds can be thousands of years old, far older than would be extrapolated from the rapid rates of shell loss detected in short-term experiments. An extensive shell-dating program on the Southern California (USA) shelf permits rigorous modeling of the dynamics of shell loss in the mixed layer, discriminating the key rates of carbonate disintegration and sequestration for the first time. We find that bivalve shells experience an initially high disintegration rate λ1 (∼ decadal half-lives) but shift abruptly, within the first ∼500 yr postmortem, to a 100-fold lower disintegration rate λ2 (∼ millennial half-lives) at sequestration rate τ (burial and/or diagenetic stabilization). This drop permits accrual of a long tail of very old shells even when sequestration is very slow, and allows only a minority (<1%) of all shells to survive the first phase. These high rates of disintegration and low rates of sequestration are consistent with independent measures of high carbonate loss and slow sedimentation on this shelf. Our two-phase model thus reveals significant spatial and temporal partitioning of carbonate loss rates within the mixed layer, and shows how shell age-frequency distributions can yield rigorous and realistic estimates of carbonate recycling on geological time scales.