Some more info please. Do you shoot in Jpeg or RAW? What post processing (if much/any) do you do (tinkering in photoshop) ? What were your camera settings ? (shutter speed/aperture, ISO, etc). What other parameters have you set (if any) on the camera? (modes). I follow you set it for auto..but if you are using Jpeg there are some other choices you have (in the camera). Shooting RAW will allow you to gather the most information without loss (losslessprocess). You will however have to do much more post processing in photoshop (or like software).
Many digital SLRs are set up for the "advanced" photographer and do not have many characteristics boosted (contrast, hue, saturation, sharpness etc) boosted in the camera. The advantage (for the advanced photog) is to set these parameters themselves in post production. Most digital SLRs will recquire some boosting of saturation...contrast etc if you don't program your camera to do so from the start. If you use RAW..it doesn't matter what you set the additional settings for in the camera...as it will ignore them for the most part. RAW is the way to go IMO...in that it will record the most digital information. What you do with it afterwards (in PS) is your choice. Do not feel bad if your pictures right out of the camera are washed out..flat..colorless..fuzzy..blurry..and not kick butt. This is typically normal for a digital SLR. All these parameters need to be manipulated in your post production software. IF you are wondering why your inexpensive point and shoot seems to give you better pictures right out of the "box"..it's because of the filtering that is applied to the better digital SLRs. They do require some tinkering after the shot (unless you program these boosted parameters in before hand...and they only work in Jpeg).
Like Bingo said...use a tripod. You also want to find a happy balance between ISO speed/shutter speed and graininess in the image. You should be shooting at a high enough shutter speed to stop action (fish) and camera shake. What lens are you using? You might also consider investing in an electronic shutter release (find 'em on Ebay for like $20). This will also help reduce camera shake due to shutter movement/bounce.
You also might consider using a flash unit. Preferably an "off camera" unit or strobe. You will "usually" get best results if you can trigger the off camera flash from the top (over subject) of the aquarium. If this is not possible..whatch out for the reflection from the glass. I prefer to avoid the flash (if possible) and use a higher ISO (800-1600) and deal with the noise in PP.
You might also try bracketing your shots until you get use to the exposure settings on that new camera. Many overexpose. If you are really serious about this photog stuff..do a google search for exposure compensation rules/techniques. Also check into "white balance" info...and a technique refered to as "exposing to the right". (right of the histogram). Lots to learn about these new fangled cameras. The best way is to shoot..shoot..shoot...and take some notes to your results.
The last (an one of the most important) things you want to do is sharpening. You want to save this adjustment for LAST. Do all your cropping, resizing, boosting of parameters, etc. BEFORE you do the final sharpening of the image. You can do a search for verious sharpening techniques (if you don't already know them). Many prefer the USM (unsharp mask) in PS. The new CS2 has a "smart sharpen" feature that also works well in certain situations.
Good luck.
BMP