Fish assemblages in tropical habitats like coral reefs or seagrass beds vary with natural cycles (e.g., lunar, diel or tidal) on several spatio-temporal scales. However, the dimensions of these variations are rarely being quantified despite their strong implications for ecosystem functioning and conservation of exploited stocks. Ignoring these predictable changes hinders the identification of structuring forces of fish assemblages and may lead to incorrect interpretations of the results and evaluation of habitats. To assess natural variation on short timescales, fish assemblages at a small tropical island (Chumbe Island, Tanzania) in the western Indo-Pacific were investigated and compared among two coastal habitats (coral reef and seagrass bed) at different lunar, diel, and tidal phases using underwater visual census methods. Results of multivariate analyses suggested two distinct fish communities in the two habitat types with the coral reef comprising a higher species richness and heterogeneity than the seagrass bed. In the coral reef, community composition and trophic diversity was influenced by all three natural cycles, while in the seagrass bed they were mainly driven by tidal phases. Mean fish densities were slightly different in the two habitat types during daytime but increased significantly in the seagrass bed during twilight hours. For the investigated habitats on Chumbe Island our results indicate that (i) through their routine migrations mobile fishes can provide important functional links between habitats, (ii) seagrass beds have lower species richness and diversity, and emphasize that (iii) fish movement governed by natural cycles can cause predictable short-term variations in fish communities.