I just came across a few documents today (dated April 2007) which detail the possiblity of a Toronto Aquarium. The developer is Oceanis Australia Property Group who are developing similar facilities in cities around the world (Dubai, Abu Dhabi, Hong Kong, etc.).
At this point, all I have is some basic renderings and a site plan but from that it looks like architectsAlliance will be handling this one. It is a three level space with a huge glass facade facing south.
The site they have picked out is at the base of the CN tower, north of Bremner and west of the Convention Center (Can someone get a Google Earth screenshot of this?).