Timed shutter, duh. I was taking the shots barely pressing my finger on the shutter button to avoid shake thinking to myself "I wish I had a remote for this thing!"
I have never used custom WB. Do you calibrate with a gray/white card according to your tank lighting, then?
I set the shutter speed was as fast as I could go with each shot, but my lens is pretty slow. f5.6 when it's fully zoomed in. Fully open it's f3.5. I had to go pretty slow on the shutter speed (60) to get many of the shots but then got that little halo from shake I think. Have you ever tried any other lighting besides flash? Like (this is kinda sad, but only other supplemental lighting I can think of right now) a shop light or something? Would that irritate the fish/coral I wonder?
Just FYI, the wireless remote for the D40 costs like $15 new. It's infrared so it only works from in front of the camera, but you can bounce it off the aquarium glass from behind the camera and it will work.
Your camera has RAW mode, so I'd use that instead of setting the custom white balance. I use Photoshop to adjust the white balance, but I'm unsure what other (cheaper) options there are for editing RAW images.
I avoid using the flash at all costs with aquarium photos. It washes out the colors and generally makes it look horrible, especially the built-in camera flash. If you use an external flash and point it down into the water from above, it looks a little better. Still, shooting without a flash always looks better to me.
Your lens is definitely not ideal for aquarium photography. It's too bad you got the D40, because the 50mm 1.8 AF lens is very good and very cheap, but it won't autofocus on a D40 or D60. That's one of the big reasons I got the D50 instead. I'm not sure what other cheap options there are for a good aquarium lens. You definitely don't need a macro lens to get great results. Macro lenses are not very easy to use for shooting fish in my experience. Great for closeups of corals and inverts, but not so much fish. You can try the 50mm AF lens and just manual focus it. That will work fine for all but fish photos. They sell for $110 brand new. I got mine for $60 used on Craigslist.
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