Anthropogenic land development adjacent to the Great Barrier Reef (GBR) has been implicated in increasing levels of sediment, humus and nutrients being discharged downstream, thus increasing the fertility of the water column and lagoon sediments. We investigated the effects of elevated nutrient (nitrogen: N, phosphorus: P) levels on ciguatera associated dinoflagellates: Gambierdiscus toxicus, Prorocentrum spp., Ostreopsis spp., Coolia monotis, Sinophysis spp., Amphidinium spp., Scrippsiella spp. and Gymnodinium spp., on host brown algae Chnoospora implexa, Sargassum spp., Colpomenia sinuosa and reef flat sediments of Heron Island. Total dinoflagellate abundances within fertilised aquaria increased by 25%, 35% and 64% on Chnoospora implexa, Sargassum spp. and Colpomenia sinuosa, respectively. Prorocentrum spp. constituted up to 60% of the total dinoflagellate population of which P. mexicanum was the dominant species. On the reef flat, total dinoflagellate abundances were an order of magnitude lower than aquaria although fertilisation increased total dinoflagellates abundance by 8% and 19% on Chnoospora implexa and Sargassum spp., respectively and decreased by 45% on Colpomenia sinuosa. Prorocentrum spp. constituting 46 % of the total population of which P. lima was the dominant species. Total dinoflagellate abundance increased by 72% in the enriched sediments of the reef flat and by 58 % in the aquaria sediments. Prorocentrum lima and P. mexicanum are highly sensitive (P<0.01) to elevated sediment nutrients. Increased downstream and point source nutrients from anthropogenic and agricultural developments into the ecosystems of the Great Barrier reef may ultimately be a direct link to additional outbreaks of ciguatera.