I think like Sunee said it's a depth of field issue. I've got a close up filter too but haven't tried it in the tank. Still, outside the tank, I get similar results to you - the depth of field is just insanely shallow (it's a 4+). The only thing you can do really is take the shot at the highest f-stop you can and with the shortest focal length lens you have (or a zoom at it's shortest setting) both will give you a greater depth of field. The trade off with the f-stop is exposure time, so a tripod would help lots with those longer exposures, though it's amazing what you can do with a beanbag, books or any other random stuff you have lying around, if what you're photographing doesn't move around too much.
There's a setting on my ancient eos 350d that has the camera try to get you the best depth of field automatically (labelled A-DEP on the main rotating selector dial on the top right of mine) - may be worth a try...
Failing that the old faithful solution is to pretend that's what you wanted!
I think the ultra short depth of field looks quite good when you use it to highlight the particular part of the shop that is of interest. Just be careful about selecting your AF points to make sure the camera is focussing on the exact area of interest since there's little latitude if the camera picks the wrong place.
For what it's worth I really quite like some of your shots.. If only there was enough light in my tank to take some shots that didn't look really dim or have blurred fish..