Fairly often I'm asked (or more accurately told) 'if an estuary will hurt the bat colonies, you must support the lake option, right?'
My answer? The one I have given for the past 5 years: I can't endorse either option -- the managed freshwater lake nor the engineered estuary -- until there is a science-based discussion about the fate of the large congregation of reproductive bats who have found refuge in this remnant of freshwater habitat, water which sustains thousands of mothers and their nursing pups (yeah, I do it in one breath). I can't support a saltwater option unless a serious discussion about mitigating the effects on the bat maternity colonies has occurred, and reviewed by qualified professionals. A science team, not a policy team. This seems reasonable, but this request has never been acknowledged. The record shows that this, its not just some last minute "hey, what about the bats?" The can of worms is that it's not just the bats that have been brushed aside... but they'll do for a scapegoat if needed.
Parts of the engineered estuary proposal reminds me of using bio-fuel for transportation: the idea is great, but the details are really messy.