Debbie, Yes the pumps are off. I also try to get the lense up as close to the tank as possible, carefull not to bang it on the tank.
The Chalices were about 2 inches away from the glass so that helped a bit, any further I'd think the shot would get blurry, Not sure though.
Brian, To get a large picture, set the compression/recording pixel. check on pg 36 of the manual. Here are the settings that I tried. M1 recording pixels and Superfine for compression. The only software I use is MS paint to crop the section of the pic I like.
I shoot in AV mode, set the ISO to 80 with aperature set to F2.7.
Select SuperMacro on the lense.
Using a tripod and timer on the camera helps lessen some blur. Another thing i did was set the custom white balance pg. 77 by placing a PVC pipe or eggcrate in the tank.
The Canon S3 is great for beginners and takes decent Macro shots with out a Macro lense.