@irontoenail - Re-populating the waters with the right kind of animals can be important too. I watched a documentary a while ago where they were investigating the impact of salmon extinction in several riparian ecosystems. Usually the salmon would make their way up the streams to lay eggs and then would die there.
The researchers left salmon carcasses in some streams and not in others and discovered that it made a massive difference in the amount of growth and diversity in the area, because the salmon provided nutrients that weren't otherwise available.
It just shows how a single component of the riparian zone can be more important than you might expect.