The limitation of the Geneva Convention, and "International Law", is that there is nobody to enforce it, and there never will be. Such is the nature of laws, which are merely the ideas of some people about how other people should conduct themselves. For better or worse, who governs the seas is the outcome of wars.
Nothing will protect natural habitats in times of war, since war is the suspension of the compact of civilisation. The most you could hope for would be that the victors of your next war are environmentalists who are happy to spend whatever it takes to clean up the mess.
This might be an argument in favour of arming Greenpeace.
-- Political Science 101