I have photographed different type of fish in different tanks, with or without flash, through the surface of the water or through glass.
However, I think I am missing something. There may be tips or hints that can make working with fish easier.
I photographed small fishes, inch-long fishes, and also Betta, which is a one to two inch long. I do have a macro lens with USM. (Canon EF-S 60mm f/2.8 USM) and flash.
However it is still very hard to focus on the fish. f/2.8 is not an option since almost NOTHING will be in focus. Even with USM and all cross-type focusing points, the fact that the fish is swimming almost constantly can proved to be tricky.
I have observed that certain fish at certain time of day will be more calm. However I can easily shoot 200 photos with only 3-5 satisfactory shots.
I also use flash, this so far seemed okay, the fish were never too disturbed by the flash. I do not think it would harm them either (vs cat with super light sensitive eyes)
So I would try to use f/5.6 or f/8.0 to get more DOF, flash, and use ONE fixed focus point (auto AF point selection will often mess things up as experience shows)
Shooting through glass is okay as long as the glass is flat and smooth (bowl-shaped tank is a definite NO due to uneven surface). Shooting top-down also gives high quality images as long as the water is still.
Still, success rate is pretty darn low.
Any advice from experienced pet photographer that has dealt with small fish, or just aquarium in general?
I like this shot because of how elegant they look, and how happy and free they seem, and the lines their slender bodies form:

(source: gapton.com)
My beloved Betta named Bubu who died to a disease after 1.5 years of keeping. [Lightened a little as suggested, didn't have time to clone out the dust yet]

(source: gapton.com)