What you can do does depend on both your camera and fish.
Fast moving fish I find it's easier to put the lens right on the glass and use the flash as they swim past. That way you get no reflection from the glass, but the flash 'freezes' the fish.
If you have fish that will pose, then no flash is needed and they wont blur in the longer exposure time thats needed.
Druu is right about the lighting though, turn off the room light to reduce reflections from the glass. If you are trying to use the flash from a distance then shoot at a slight angle to the glass, reduces the flash reflections
Ohh.. and clean the glass
Cheers
Ian
Some examples.. Lens on the glass and flash on.
Back from the glass, but shoot at an angle.. Note the glass NEEDS to be cleaned
No flash.. lens on the glass. But the fish is still and just watching so the 20th sec exposure doesn't matter. Only room lights on to encourage shy pleco out.
Now.. go and take HEAPS of pics till you get it right
Cheers
Ian