Zonation of macrobenthic communities (corals: algae, molluscs, sponges and echinoderms) on fringing reefs was investigated in two bays in a coral reef ecosystem (Moorea, French Polynesia). Species richness, abundance and coral cover, and species richness of macroalgae increased from the bayhead to the bay entrance. For molluscs and sponges, no general trend was observed. Species richness and abundance of echinoderms increased from the head to the entrance of Opunohu Bay, but this trend was less pronounced in Cook Bay. The gradients observed for corals, macroalgae and echinoderms were correlated with one or several of the following abiotic factors: salinity, turbidity, concentration of silicates in surface waters, and concentrations of organic carbon, carhohydrates and amino acids in the sediments. These factors are associated with terrestrial run-off via river discharge that occurs at the bayheads, where the major river is located. The high degree of confinement in the bayheads allowed the establishment of only a few tolerant macrobenthic species. Although the low diversity and abundance of corals and echinoderms seem to be a characteristic of Polynesian bays, a high diversity of corals can be found in the vicinity of the bayheads in coral reefs of the western Pacific. (C) 2000 Academie des sciences/ Editions scientifiques et medicales Elsevier SAS.