"Environmentalists" also made a big fuzz about the Øresund connection, claiming that the artificial island midway would disrupt the entire Baltic Sea ecosystem by drastically reducing the flow of water.

Didn't happen. The (fairly small) compensatory digging had the effect the engineers had calculated and the water flow actually increased slightly and the Baltic Sea ecosystem is fine -- or at least not harmed by this particular project.

I think we should trust the people who can (and do) make calculations over those who can't (and don't).

The tunnel will very likely be less disruptive to marine animals than ferry boats. During the construction yes it will be worse but 10 years after? The ecosystem will have forgotten the disruption and will have gained additional peace from reduced/eliminated ferries.