Day-night changes in fish communities were quantified in 6 associated shallow-water biotopes within a single bay: mangroves, seagrass beds, algal beds, channel, fossil reef boulders, and notches in fossil reef rock. All biotopes, except the algal beds, showed a strong reduction in fish density and species richness at night, caused by absence of diurnally active fishes and migrations of Haemulidae and Lutjanidae to the seagrass beds. The fish fauna of the different biotopes showed a relatively high dissimilarity between day and night. This dissimilarity is largely caused by absence of Acanthuridae, Chaetodontidae, Labridae, Pomacentridae, Scaridae and Sparidae at night. These fishes seek shelter at night in, amongst others, the channel, notches and boulders. The balloonfish Diodon holocanthus utilised almost all biotopes as shelter as well as feeding sites. The wide distribution of its preferred food (molluscs) probably explains its distribution in most biotopes at night. The nocturnally active Haemulidae and Lutjanidae, on the other hand, migrated from their daytime shelter sites to the seagrass beds at night to feed. Some of these fishes also migrated to the algal beds to feed. The preference of Haemulidae and Lutjanidae for the seagrass bed as a feeding biotope, instead of other bay biotopes, appears to be related to the relatively high availability of their preferred food (Tanaidacea and Decapoda) as determined by digestive tract analysis. Other bay biotopes showed much lower densities of such food items compared to the seagrass beds.