The Belize atolls-Glovers Reef, Lighthouse Reef and Turneffe Islands-show differences in geomorphology, lagoonal depth, bottom sediment, growth of mangroves and sea-grass, exposure to waves and currents as well as in their sedimentation rates and their age. Bivalve shell assemblages in lagoonal areas reflect these geomorphological differences. On each atoll, 32 to 44 recent sediment samples were taken (total number of samples 111) and bivalve shells subsequently identified. The resulting database (32,122 bivalve shells in total) was analysed using Q-mode cluster analyses. Both the distribution of species characteristic of different lagoonal habitats and the distribution of bivalves with different life and feeding habits were investigated. Epifaunal suspension feeders were found particularly on hard-bottom along the reef-crests or clinging to mangrove roots. Infaunal suspension feeders show a more diverse distribution. Deeper lagoonal parts and areas with mangrove growth are often inhabited by chemosymbiont-carrying bivalves, indicating locations of reduced sediment. Deep burrowing detritus feeders are very abundant in shallow-water areas with moderate to high water agitation and were seldom found in Halimeda-rich sediments.