I can't speak directly to aquariums, however I've done shots at zoo's before. When things are enclosed in glass, you tend to have problems with glare. Especially from flash, but also from other sources, it can make getting a shot very difficult. The one trick I've learned is to find off-angles from any intruding light sources. The general idea is that light bounced strait on will bounce strait back, so if you need to use flash, point it at an angle to the glass so any reflected light bounces off and away from the camera. It can be tricky to position yourself for the best shot, as you need to take the same bounce angle into account for any other light sources.
I also highly recommend using at least an f/2.8 lens, however faster lenses would be even better. A wider max aperture will allow more light through in less time. High ISO performance is probably your best tool, though. A camera that can handle ISO 800/1600 (or better) without too much noise is going to give you the best chance of capturing good shots.