Aquarium Photography Tips

A few ideas:

• Get a better camera
• Disable the flash unless you have an off-camera flash.  You may need to correct the colour balance depending on your camera/lights.  If your camera can't do this, there should be an option in your photo editing software
• If you don't have photo editing software, get some.  There are plenty of free products around
• Use a tripod
• Set the ISO on your camera to it's highest setting if you have the option
• Set the resolution to it's highest setting
• Don't get too close unless you have a macro option
• Don't use the macro option unless you have a tripod

...
There are two basic forms of autofocus; active and passive.  Solutions to your problem depend upon which one your camera has.

• Passive uses software in the camera to analyse something about the picture, it may be contrast or colour or phase of the light.  It uses this info to focus the lens.
• Active uses a beam of light, usually infra-red, fired from the front of your camera and detects the echoes bouncing back from your subject.

Cheaper or older cameras will choose one or other of these systems, more expensive or newer cameras will have both.  They will use passive autofocus until the light level drops below a threshold and then use active autofocus.

Forgive all this preamble, but the problem you have can have different causes or solutions depending upon this info.

Active autofocus is the most likely system to be banjaxed by use through glass.  The infra-red is reflected from the glass and the camera thinks the glass is the subject.  The only way to get round this for aquarium photography is to move back a foot, depress the shutter halfway and then move forward a foot.  On  most cameras, this should lock the autofocus.  It's crude but...  For other photography there are alternative solutions.  I had this problem with a 35mm compact camera I used to take on skiing holidays.  Taking photos of the mountains through the window of the cable-car would focus on the glass not the mountain.  The solution was a piece of masking tape over the infra-red emitter.  The AF system would then focus on infinity and my landscapes were in focus!
Passive autofocus is more robust because it is analysing the image entering the camera. Two things can screw it up.  First, insufficient light.  This is a problem we will be coming across again and again photographing our fish.  Second, sometimes the AF system can be fooled if there is any dirt or dust on the glass.  This is easy, you should be taking photos through clean glass anyway.  (That's clean on both sides).

Hope SteveS is OK with these gems being resurrected here. 

Because I have no idea how to use the camera (it's an old Fuji S7000 that used to be my husband's) I use the following settings:
On the mode dial I use the auto setting (other settings are aperture priority, shutter priority etc)
I use the macro button, but press it only once as twice is for just a few inches - I use that for my African violet flowers as in my avatar.
The focus mode selector switch is set to continuous.

...  More interesting is the fact that your camera has a preprogrammed "Aquarium" mode! (page 69-72)