Fish species are for example disrupted by water dams.
I know you said Dams and not weirs and not run of river plants, and big dams have their issues, but not on the same scale as the oil industry.
There is a nice reference list, including many English language reports at the end of this report from the Swedish Agency of Marine and Water Management. [1]
I think they summarise it nicely by saying “Hydropower is one of the biggest impacts on the ecological status of a river. At the same time it is one of our most important energy sources.” [in Sweden]
Sources:
[1] https://www.havochvatten.se/hav/uppdrag--kontakt/publikation...
As I understand it a lot of the downstream ecological effects rely entirely on the fill rate the Ethiopians choose (3 years, 5 years, 10 years, 15 years, etc). A fast fill rate (5 years or less) could have significant short to medium term effects on the arable land downstream in Sudan and especially Egypt.
The dam is oversized for its power output (to ensure it can meet peak output demands during the wet seasons) and will operate as a fish trap, cutting the number of fish able to head downstream (and ultimately to the sea / mouth of the Nile) by a significant amount.
[1] https://en.wikipedia.org/wiki/Grand_Ethiopian_Renaissance_Da...
Even at large dams it is possible to build fish ladders to allow migration.
When we were filling our head ponds (reservoir) we weren’t allowed to impound more than 10% of the total flow in the river.
That said, there are many low head dams built exclusively to extract power, and many of those are no longer serving a useful purpose.
Also, in some sense, wind and solar power aren't fully "green" energy because they require giant turbines and solar cells that require a lot of polluting to make, maintain, and eventually dispose of. We still, of course, seem to consider them to be green and beneficial, I assume because someone has done the calculus to see that the costs of their pollution is less than the benefit of their use. I'm willing to bet that many dams are similar.
The best kind of dam from the point of view of the power utility is one that allows the water flow to scale freely from zero to overwhelming to match electricity demand, and never allows water to bypass the turbines. But that's an extreme, not the only kind that makes financial sense. If you both reduce the time flexibility and also allow some water to bypass the turbines, you can usually get most of the power at a small environmental cost... usually, not always.
While the dams were built inside very preserved forests, so there was initial damage, the surrounding area (tens or hundreds of sq. km) were put under protection to guarantee the water supply, so no reforestation, no agriculture, etc. Now even the surrounding areas are in better shape today than in the 1960s when the dams were built.
Of course it helps the individual size of each plant is small (tens of MW, tops).
The fact that it damages an ecosystem does not count there. Moreover, the fact that dams damage an ecosystem have very little bearing on the global-warming effects of dams.
Whilst I do not want to say that ecological damage is not important, I think it is an issue that 'green' and 'ecological' have dual meanings. The current main usage being "Does not cause greenhouse gasses" with a less used original meaning of "Is good for the environment". This causes a lot of friction between people who use the same words but care differently about environmental impact beyond global warming.
It used to be that caring about the environment was a fringe movement in so far as getting political change. Global warming has gotten 'being green' on the political agenda. But it sometimes feels like some of the more extremist green ideas have snuck into the greater public discourse under the guise of being 'green'.
For run-of-river hydro power, one mitigation is fish ladders:
A dam changes the eco system, but nature forms a new balance around the new geographical feature that is not inherently worse, just different.