lots of factors to be taken into account:
1. Glass and water to shoot through
2. Fish that keep moving (!)
3. Light reflected off the glass
4.Delayed reaction of digital cameras
From my limited experience the best way is by using only the aquarium lights
and getting the front of the lens as close to the glass as possible; try to
focus the camera on the subject fish, and use as wide an aperture as you can
to eliminate dirt and such like on the front glass of the aquarium.
I saw mentioned in a photography magazine recently that the best way they
had found was to use an off camera flash gun resting on the plastic lid that
protects the aquarium lights from the water - no idea how well that would
work though. I might add that some fish may be sensitive to flashes so observe them for the first time.
There are a couple of sites on the web that might help: