Macroalgal-dominated reefs are a prominent component of tropical seascapes providing food and shelter for many species whilst subsidising secondary productivity in coastal ecosystems. Monitoring and managing macroalgae require an understanding of key processes that alter these assemblages, especially at the local scale. Here we consider how sediment depth/cover and abundance of the urchin Tripneustes gratilla influence variation in community composition and physical structure of macroalgal patches within the World Heritage listed Ningaloo Reef, Western Australia. Our study found high urchin densities in sites with lower sediment cover and depth and that sediments, urchin abundance, and seascape position explained 32% of the spatial variation in macroalgal community composition with a greater occurrence of Sargassopsis, Caulerpa, Sirophysalis and Hormophysa in the lagoon where sediment cover/depth was high. Canopy height and cover of canopy-forming macroalgae were also greater where sediments were high and urchin abundance low. Macroalgal genera with a strong and robust thallus were found in sediment depths up to 6 cm as opposed to those with softer, fragile thalli that were found in sediments < 2 cm. Our results demonstrate that high densities of urchins and mobile sediments can have profound effects on the composition and structure of tropical macroalgal assemblages. Changes to macroalgal community composition and physical structure will have flow-on effects for ecological processes such as productivity and habitat use which can alter the ecosystem goods and services macroalgal-dominated habitats provide.