Tropical habitats and their associated environmental characteristics play a critical role in shaping macroinvertebrate communities. Assessing patterns of diversity over space and time and investigating the factors that control and generate those patterns is critical for conservation efforts. However, these factors are still poorly understood in sub-tropical and tropical regions. The present study applied a combination of uni- and multivariate techniques to test whether patterns of biodiversity, composition, and structure of macrobenthic assemblages change across different lagoon habitats (two mangrove sites; two seagrass meadows with varying levels of vegetation cover; and an unvegetated subtidal area) and between seasons and years. In total, 4771 invertebrates were identified belonging to 272 operational taxonomic units (OTUs). We observed that macrobenthic lagoon assemblages are diverse, heterogeneous and that the most evident biological pattern was spatial rather than temporal. To investigate whether macrofaunal patterns within the lagoon habitats (mangrove, seagrass, unvegetated area) changed through the time, we analysed each habitat separately. The results showed high seasonal and inter-annual variability in the macrofaunal patterns. However, the seagrass beds that are characterized by variable vegetation cover, through time, showed comparatively higher stability (with the lowest values of inter-annual variability and a high number of resident taxa). These results support the theory that seagrass habitat complexity promotes diversity and density of macrobenthic assemblages. Despite the structural and functional importance of seagrass beds documented in this study, the results also highlighted the small-scale heterogeneity of tropical habitats that may serve as biodiversity repositories. Comprehensive approaches at the "seascape" level are required for improved ecosystem management and to maintain connectivity patterns amongst habitats. This is particularly true along the Saudi Arabian coast of the Red Sea, which is currently experiencing rapid coastal development. Also, considering the high temporal variability (seasonal and inter-annual) of tropical shallow-water habitats, monitoring and management plans must include temporal scales.