Bunurong aquarium in Frankston is great for freshwater, I have also heard good things about another store close to Bayside Frankston which stocks a lot of interesting bottom feeders
For saltwater, mentone aquarium or reeflections near Southland.
The only aquarium close to the CBD is the store near Queen Vic market, which provide awesome advice and have a great fw section.
Happy fish finding, will be keeping an eye on this thread to see more local suggestion!