Careful control is done in evaluating the treatment options for things such as the sea lamprey program. Right now, they're moving away from chemical treatments. In the past they relied on using a chemical called TFM, which was a piscicide: it killed things. Now they're moving toward things such as a sterile male program and pheromones, which are natural body odours, to attract lamprey. They only attract lamprey and nothing else.
Moving to these new strategies should have much less effect on non-target species. But, certainly, any of these managed control programs have been very careful to try to ensure there wouldn't be an impact.