I think the answer is that it depends where.

I haven't heard of any coral reefs at the Sea of Cortez, which is one place they're considering desalination, for Arizona (importing water from Mexico).

Edit: I checked and there are coral reefs along the Sea of Cortez. :) I don't know where would be safer to do it, but I'm sure it makes a difference where. And sadly it may not be as important at places where we've already destroyed the habitats.

Edit 2: Some are very concerned about its potential effect on Sea of Cortez: https://tucson.com/opinion/local/local-opinion-desalinating-...