If an entire river is completely transformed with rocks all over the show in weird ways for like a mile, sure, you may well be upsetting the ecosystem in some way. If this happens in a couple spots on a river, the impact will be negligible. And they're just rocks, a new arrangement will make new habitats for different local lifeforms.
Don't forget that humans are in fact also a part of nature, we've been world-wide and in our modern form for like 200k years, nature has had time to adapt to low-scale low-technology human impacts.
Not without human interference. But my point is homo sapiens and ancestors/relatives have been doing stuff like 'stack rocks' for well over two hundred thousand years, quite plausibly two million plus years, that is basically nature.
I struggle to believe there's evidence that moving some rocks has any non-negligible effect on local populations or biodiversity. Life is very, very, rarely as fragile as you describe. But please share if there is indeed such evidence and I'll change me mind.