I think one of the key issues is how persistent you think the impact will be. For example, some activities, including waste-water discharge, are regulated. In some cases, when the licences for either waste-water discharge or an oil platform expire, the idea is that those will be removed.
If you are confident in the removal of that existing activity, you could go ahead and make a protected area, knowing that at some time in the future those systems will become more natural.