As Danielle said, it won't affect the colours unless you are swimming either deeper (5m to 10m down and more) or in a pool with a lot of blue tiles.
When going down the water column, the colours start disappearing starting with the longer wavelengths. So red will be the first to go (startig to get noticeable at about 5m to 10m), then yellow, green and finally blue. At least as long you are in crystal clear (sea)water, otherwise, especially in fresh water, the ever present algaea will give the water a greenish tint, even if the visibility is good. This will act a little like a colour filter emphasizing the green instead of the blue and kicking in much more shallow (3m or so, depending how much algea). But red will go first nevertheless.
When swimming in a blue tiled pool, vertical absorption of colour is not that much of a problem, as they are usually not more than 5m deep and have super clear filtered water. What will matter is the colour spill, as the light scattered back from the blue tiles has a blue tint, which emphasizes blue over red and will "spill" on your tail. Colour absorption of the water itself will matter though, even in a pool, when doing shots from a horizontal distance. There too red will start getting filtered at a distance of about 6m to 10m between you and the camera.
So, to sum it up, yes, the colours will start to get lost, but is a very gradual process and won't matter in a pool or when swimming near the surface (about 2m to 3m down).
When doing photoshoots, especially at depth using only ambient light, this is another issue, and there too Danielle is correct. An underwater photographer will know about it and how to counteract this. Colour filters and post-production will only get there up to a certain point, though. Especially at depth you have to bring your own light with you and be more or less in the limelight, so to speak. And then having a tail with your colour scheme will be of advantage, as you are the only thing with reddish tints to an otherwise blueish background. You will literally pop out and shine, but not so much that it looks artificial.
So, time to stop rambling, the post is long enough already. Long things short, don't think too much about the colours in the water, choose the scheme you like.
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