About the other species in the lake, before an application of rotenone is implemented, you capture all the native species and hold native species off site while the application is administered, which takes a day. It will be effective for about a week or so afterwards. After that, the level drops and those species can be put back in. This doesn't affect any of the insects or the aquatic life in the lake—just the fish.
In the outflow, rotenone can be neutralized with potassium permanganate. You would treat the outflow water to make sure that none could get to the Miramichi River.