Taphonomic signatures on modern bivalve shells, such as traces of drilling organisms, encrusters, fragmentation, and abrasion function as indicators of environmental differences on Belize atoll reefs. Glovers Reef, Lighthouse Reef, and Turneffe Islands are three adjacent Caribbean atolls showing variations in geomorphology, lagoonal depth, sedimentation, mangrove growth, sea-grass cover, and exposure to winds and currents, as well as differences in their lagoonal development and age. A variety of bivalve assemblages characterize lagoonal subenvironments and also mirror the above-mentioned environmental variations. Taphonomic signatures, such as shell-size distribution, disarticulation, sorting, boring traces, encrustations, fragmentation, and abrasion, were identified on bivalve shells from a total of 111 surface sediment samples. Shell-size distribution and sorting of right and left valves indicate in situ deposition of populations on each atoll. Increasing residence times of shells on the sediment surface due to decreasing sedimentation rates from Turneffe Islands to Lighthouse Reef to Glovers Reef cause an increase in taphonomic shell signatures.