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It's hard to get a real accurate vote because very few people are Aquarium fanatics who travel around visiting all or even most of them. Most folks if they're lucky only get to see a couple.
That being said, when you consider the size of Chattanooga, their Aquarium is a huge accomplishment for a city of that size, and I'm pretty impressed with it. It now has two buildings, sits in the edges of the Tennessee Riverfront park downtown, and has a lot of more natural "habitat(ish)" rooms inside with fake waterfalls, trees. In some ways it almost has Flora conservatory qualities mixed with an Aquarium - pretty neat. Plus you can walk to a variety of other things (restaurants, clubs, the River, etc) without getting attacked by bums.
Our Georgia Aquarium in downtown Atlanta I have to say, for me, is a bit of a disappointment. It's billed as the "worlds largest", but really that's because it has the most WATER in the tanks (around 8 million gallons), not necessarily due to the grounds, walkable areas, etc. Many people complain about several areas inside that "bottleneck" and were poorly laid out to handle large crowds (and there are ALWAYS large crowds), and some of the smaller exhibits have tiny viewing areas. The only thrill parts are when you're in the underwater tunnel and the Whale Sharks swim above you (but you're squished in the throngs of people), and the Beluga Whales. The Dolphin exhibit coming next year is a bit controversial - some feel they should only be in places like Seaworld where they are rehabbed, etc., and not in a tank at an Aquarium. I tend to agree. The area around the Aquarium is building up with various things, but there is still a very heavy "bum element" in downtown Atlanta that turns a lot of people off, and discourage you from walking around to see other sites once you leave the immediate area.
So, when I have free time and am in an Aquarium mood, I do tend to drive the 2 hours North to Chattanooga to spend the day in theirs, rather than the 45 minutes East to the Atlanta facility. Sorry.
Here's a small number of photos/videos I've taken at each:
I've been to Atlanta's, Vancouver's, New Orleans', Monterey's, San Francisco's, Honolulu's, and Chattanooga's, and my favorite wasn't on the list.
The Oregon Coast Aquarium at Newport, Oregon. Seriously cool. Wonderful place, real variety and great exhibits. Got to see Keiko (the "Free Willy" killer whale) a couple of times there--of course, that was the highlight for my (now grown) kids.
I really, really liked Chattanooga's as well. One big reason is that is has a completely different emphasis than most--freshwater. As already stated by AtlantaGreg, it's got some great habitat rooms--and it's huge.
Chicago's aquarium = best by far. Not to mention, you could always go scuba diving in Lake Michigan I suppose if you really wanted to see an aquarium in the wild hehehe.
The Aquarium of the Bay shouldn't be the choice for SF...it's in pier 39, and is pretty much a tourist trap, and really not that impressive. SF's aquarium for the poll should be the Steinhart Aquarium at the California Academy of Sciences, in Golden Gate park.
Best I've been to is Shedd in Chicago... not really an aquarium person... tried to go to ATL when it first opened around nye 2006 but couldn't get tickets.
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