1.Populations of marine megaherbivores including green turtle (Chelonia mydas) have declined dramatically at a global scale as a result of overharvesting and habitat loss. This decline can be expected to also affect the tolerance of seagrass systems to coastal eutrophication. Until now, however, simultaneous effects of top–down control by megaherbivore grazing and bottom–up control by nutrient input have not been tested experimentally. 2.We therefore investigated the interacting effects of nutrient (N and P) addition and mimicked green turtle grazing on seagrass and epiphyte productivity, seagrass biomass and nutrient contents in exclosures at a pristine seagrass site in the Indo-Pacific region (Kalimantan, Indonesia). 3.Grazing almost doubled leaf biomass production rates, while nutrient addition (N+P, slow-release granules) did not have an effect on these rates. Rhizome biomass was, however, strongly reduced by nutrient addition. In contrast to phosphorus, tissue nitrogen contents increased after nutrient addition, showing that nitrogen was not limiting primary productivity. Epiphyte growth was, however, strongly correlated with high water column P concentrations, indicating an indirect negative effect of eutrophication when turtle grazing would be absent. We calculated that green turtle leaf grazing leads to substantial exports of N and P, at rates of at least 8% of the standing stock per day equalling the daily seagrass production, up to 13 (N) and 1.4 (P) mg m−2 day−1. 4.Synthesis. By combining our quantified effects with literature data, we propose a conceptual model of seagrass functioning under megaherbivore leaf grazing and eutrophication. In tropical seagrass systems with high green turtle grazing pressure, grazing alleviates the negative effects of eutrophication by the stimulation of seagrass production and concomitant nutrient uptake, the increased export of nutrients and the indirect prevention of low below-ground biomass. Similar to the role of terrestrial megaherbivores, these strong top–down controls show the pivotal role of green turtles in current coastal systems, which is lacking in systems where their numbers have greatly declined. These marine megaherbivores do not only drive structure and functioning of their foraging grounds but also increase the tolerance of seagrass ecosystems to eutrophication.