Environmental drivers of seaweed biomass were investigated at Ningaloo, Western Australia, a coral reef ecosystem with negligible anthropogenic influences on seaweeds from fishing, farming, or eutrophication. Periodic surveys of benthic macroalgae occupying seaweed‐dominated beds within the lagoon at two locations (Coral Bay, Tantabiddi) were made during winter, spring, and late summer over a 26 month period. Canopy‐forming Sargassum spp. biomass fluctuated over a seasonal growth—decay cycle, with highest values in the warm summer months (up to 1013 g fresh weight 0.25 m−2 at Coral Bay) and lowest values in winter (down to 155 g fresh weight 0.25 m−2 at Tantabiddi). Conversely, prominent understory seaweed genera Dictyopteris and Lobophora reached peak biomass in winter, when the Sargassum spp. canopy was lowest. Sargassum spp. biomass variation could be attributed largely to time (52%), location (21%), and site (26%), with low variation within individual seaweed beds (1%). Statistical analysis of the influence of five environmental variables (temperature, light, wind‐driven upwelling, rainfall, significant wave height) indicated that location and sea temperature (1 month antecedent to biomass) provided the best explanation for Sargassum spp. biomass fluctuations. While sea temperature is a key driver of seaweed temporal dynamics, heterogeneity at the kilometer scale suggests that spatial context is also important. Given the important role of seaweeds in many ecosystem processes, this strong biophysical coupling between Sargassum spp. biomass and sea temperature suggests that thermal climate change will significantly affect coral reef productivity and biodiversity.