Last I was in an aquarium I regretted I only had my point and shoot camera, as I would have wanted to use Raw and manual settings.
I went with P mode and no flash, and I also pressed the lens against the window to avoid reflections. It is also a good trick to hold your hand around the lens and the window you are shooting through. Otherwise, you can save good images by retouching them.
Another thing , which is true in all hard conditions: take A LOT of photos. Most of them will look blurry and not where you wanted them to be.
Those creatures move fast sometimes and you need to start shooting at 3-6 fps before they come into the position you want. And due to the slower than desired shutter speed, you can also follow the fish you want to catch at the same speed, like manual dynamic image stabilization.
I would also use polarization filter, if the brightness allows it. Hoya HD CIR POL takes less light away (80% transmission vs 60% on most other filters).
Examples from my trip with my point and shoot camera:
Follow focus for lightning fast subject (it just dived into the water):
Hand cover between glass and lens: