Not exactly. The Nederlands is mostly locked and without it, Amsterdam would be underwater. Humans have done this before and it's not a huge issue. No one is swimming in Boston Bay anyways. Note this proposal was supposed to be for Long Island to Deer Island, then Deer to Moon if I'm not mistaken. It could've been all the way to Hull too. The body of water would be so large it would likely be fine.

Also, the alternative is we just let South Boston, Charlestown, and chunks of downtown sink over the next 30 years. As much as I totally think most of South Boston is a scam and just yuppie fast luxury homes for dumb transplants that dont know any better, I doubt we'll just let it become an intertidal zone. We're between a rock and a hard place here. Keep in mind this has been done before the Dredging Act. Back Bay was a Bay. We've rerouted and moved large bodies of water with no issues just making them artificial lakes.