The main problem I see with the expansion of boating into modest sized streams is that the boaters clear the streams of large woody debris (LWD), i.e. downed trees and logjams.
And LWD is essential to streams having good pool and cover habitat. Our stream restoration efforts should be oriented towards restoring normal levels of LWD.
And for stream management you really have to make a choice between:
1) An artificially "open" stream for boating passage.
and
2) A restored stream, with a natural level of LWD, and normal stream floodplain structure and function.
The two things are not compatible on modest sized streams. You have to pick one or the other. And if you pick #1, there is a substantial impact. To trout habitat and therefore trout populations.
But also ecological impacts that go way beyond that. (Amphibian habitats, floodplain vegetation, floodplain water tables, groundwater, wetlands, etc.) It's a very big topic.
You can have a "kayak canal" or a really healthy stream. But, you have to choose.
On larger streams, for example, the West Branch Susquehanna, you don't have that issue.
The LWD would never form a blockage that would prevent easy boater passage.
LWD on a stream like that is in the form of sweepers along the margin of the stream.