Interestingly enough, it was Thoreau's inventory of species in these very streams and tributaries as documented in _The Maine Woods_, which can tell us how we're doing with the restoration of the waterways today. Thoreau's book was comprised of notes from three visits in 1846, 1853, and 1857, and he had a pretty early and close insight as to how bad the damage was from the get-go.
At the end of the book, in the appendix, he noted several introduced species. Since he often used "Indian" guides to help him navigate upstream, he also had the opportunity to learn a bit about what species were native and what were brought in by the newcomers. (Disclaimer: my mother was one-quarter indigenous to one of the tribes Thoreau mentions, so I've studied these texts pretty thoroughly).
Several interesting musings on the encroachment of the white man into these lands; this one especially:
> Tahmunt said that he traded at Quebec, my companion inquired the meaning of the word Quebec, about which there has been so much question. He did not know, but began to conjecture. He asked what those great ships were called . that carried soldiers. " Men-of-war," we answered. " Well," he said, " when the English ships came up the river, they could not go any farther, it was so narrow there ; they must go back, go-back, that 's Que-bec." I mention this to show the value of his authority in the other cases.
[146 THE MAINE WOODS: https://archive.org/stream/mainewoods00thorrich/mainewoods00...]