A CPL will cut a lot of the glare but it's still really hard to get quality shots of fish in water if there is any tinge of colour. Crystal clear water is what you want and if it's an outdoor pond, chances are there will be detritus in the water in the form of particles and possibly algae. Also, your AF may go a bit haywire at times because of the water's surface interfering, and the fact the CPL will cut the light by two stops, making it hard for the AF to latch on. Use manual focus for best effect.
I also find that because of the focus issues, it's often best to err on the side of caution when selecting an aperture; go for more than you need to increase DoF until you are on the money every time with focussing, be it AF or MF. Just means you get more keepers.
I find the best lighting is that your get mid-summer when the sun is at its highest; winter light is never great because it's so low for most of the day (when the sun comes out).
Also, shoot when the water is at its calmest because it will lessen the number of highlights and will make focussing easier. Plus, the fish will be easier to see, unless you're going or something abstract.
If you can, try experimenting with off-camera flash positioned so it doesn't reflect back into the lens (i.e you don't get any highlights). This could really help put some light into the shot and lift the colour of the fish, especially if the base of the pond is dark, as most are.
It's the one part of my job that annoys me and when any of my editors ask for shots of fish in water, a piece of me dies!!!
