Taking photos of fish in a bucket to look at colouration changes, what do I need to consider?

So as part of my masters project I will be going into the field and catching fish. I will then be putting these fish into buckets and taking photos of them. I will then take these photos back to the lab and assess colours with imaging software (hopefully Photoshop but probably imageJ as this is free)
I will be taking these photos through the water in outside conditions with a macro lens and ring flash (however I do have another standard lens (cant remember the dimensions etc off the top of my head now but I can get hold of them if it is needed)
What do I need to consider when taking these photos so that:
1. I have minimum to no light reflectance on the surface of the water so that I take the photo through the water surface. and
2. so that colour variation between photos is not affected so that I can quantify the colour change.
I have been thinking that I might need some kind of shading or black cover to put over the whole photograph set up as to remove external light influences. Also, would a polarizing filter help with reducing/removing the surface water reflectance or would this complicate matters more with distinguishing true colours? This is very important as I do not want to have the flash or natural light reflect back into the photo to distort the light levels.

I am using a using a Canon EOS 400D digital camera, 90mm tamron sp Di 1:1 macro lens and a ring flash and will include a standardized colour chart in my photos but if I can reduce any variation in photos before I take them using a correct camera set up this will obviously take me lots of time in digitally altering colour balances. Also if I do have to digitally alter colours I am not sure of how true a representation this will have on the actual colours and so would prefer to keep this to a minimum.

Also is there anything else I will need to consider?
I will be taking another photo of each fish next to a ruler to standardise for scale with each fish so length etc can be worked out more accurately.