That is disappointing about your experience being so crowded and busy. My wife and I visited there in 2012, staying on the cruise boat for two nights and it was absolutely amazing. Almost no people and the water seemed fine, especially when we kayaked into and around the rock islands. Maybe it has changed in the past 6 years, becoming more commercial. I hope not as I would love to go back there!
RE: Ha Long Bay, Vietnam - Spectacular, mesmerizing but sadly polluted, overcrowded with tourist & too commercialized