A simple algorithm that uses MODIS imagery is developed for not only monitoring the spatial extent of Trichodesmium blooms but also for quantifying the concentration of those blooms. The results from this work support previous studies that show the new nitrogen load introduced by Trichodesmium to the Great Barrier Reef lagoon is similar to or greater than that from riverine discharges. However the current management programs aimed at improving the chronic eutrophic state of the GBR ignore the N load from Trichodesmium. These programs also ignore the fact that Trichodesmium spp. could be a source of toxins in the ciguatera food chain. A management program based on the harvesting of some of the massive nutrient-rich Trichodesmium biomass that accumulates in the surface waters and using that harvested product as a bio fertilizer is proposed. The harvested Trichodesmium would also contain valuable bio-chemicals. Such bio-chemicals if successfully extracted can demand a significant economic return. Hence a management plan based on harvesting the biomass offers a huge potential to cover the cost of the harvesting and potentially develop a new, very profitable industry as well as reducing the negative environmental impacts of the Trichodesmium blooms.