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The implementation is not entirely clear from the article, but Hydro is generally bad for the environment. Changing waterways by diverting flow or damming causes significant environmental impact.
Everything we do has an impact on the environment. The questions are whether it is less damaging than the alternative, and how sensitively it is implemented. If you run a micro-hydro system on a creek and are using a small percentage of the flow in that creek it is arguably much less damaging than buying electricity from the grid with all of the impacts associated with that (cleared land for transmission, mining for copper wires, potentially coal etc, etc)
Super cool stuff! Thanks for sharing!