The present study considered the influence of the tide on shallow water fish assemblages within the Wakatobi Marine National Park, Indonesia. Timed underwater visual observations were made across a gradient of intertidal to subtidal habitats from near-shore to reef crest at different tidal heights. Transient fish were found to dominate shallow water fish assemblages and the assemblage composition varied with tidal state. Fish assemblages were more diverse and abundant at higher tides in both coral and sea grass habitats, however, this was more pronounced within sea grass habitats. A tidal reduction from ≈2.0m to ≈0.8m (above chart datum) corresponded to a 30% reduction in fish abundance, while species richness also significantly decreased from 13.5 to 10.8 species per standardized timed observation. Fifty fish groups were reported from sea grass habitats with the most abundant being from the Engraulidae family and Lethrinus harak, which form important local subsistence fisheries. This research confirms the importance of tidal changes in structuring the fish fauna of Indonesian sea grass habitats and underlines the connectivity that exists between these habitats and nearby coral reefs.