Ecosystem modifiers have the ability to significantly alter the ecosystem they inhabit sometimes with serious consequences for their own populations. We evaluated the ability of green turtles (Chelonia mydas) to modify seagrass ecosystems by their foraging activity. This study was conducted in a seagrass-dominated lagoon in the Lakshadweep Islands, Indian Ocean, where a stable high-density congregation of green turtles is present. We determined a gradient of turtle density in the lagoon and measured the intensity of turtle herbivory across the gradient. We then measured the impact of increasing grazing on seagrass structural parameters, growth and flowering along this gradient. Our results indicate that turtles substantially change seagrass meadow structure (canopy height, shoot length, width and density), reduce flowering and can potentially even cause changes in the species composition of the meadow. We discuss the implications of these results for seagrass ecosystem function, green turtle movement and human attitudes. When conserving ecosystem modifiers like the green turtle, any management strategy needs to include a detailed knowledge of the roles these species play in the ecosystems they inhabit.