Thanks for the comments, I own a CPL but this was taken just after midday with the sun behind me, from what I've read a CPL should be used 90 degrees to the sun. I was there to shoot surfers so this one was just a bit different. If I used a slower shutter speed wouldn't the aperture open up and I would get the same shot?
In my experience there is always an effect when using a CPL, irrespective of whether the sun is shining directly onto your left or right cheek. The effect is certainly lessened, and you'll lose ~1.5stops dependant on CPL brand, but you'll certainly see the difference.
Regarding your shutter comment - you clearly have an understanding of the exposure trio (shutter, aperture, ISO) but you're only thinking of it in image brightness terms.
But, and it's a big but - shutter and aperture control two key creative effects, they aren't purely for exposure. The slower the shutter, the greater the motion blur & the faster the shutter, the more frozen your scene becomes. Aperture controls the depth of field - when you select a focus point for your image, imagine a big square window sitting on that point. When using a wide aperture, i.e f/1.4, only items through which your big window cuts will be in focus. To increase your depth of field and ensure that more of the area in front of and behind the window are sharp, you will need to close the aperture down, i.e. f/4.5. See the two images below.
You are right to say that each should remain balanced to keep a correctly exposed image - you should be using your camera's light meter to determine this. My suggestion was to slow the shutter - thus creating more motion blur in the water. The problem here is that you would've needed a tripod to keep the remaining static items (rocks, horizon) sharp. If you were dead-set on retaining the same depth of field (aperture) and my suggestion to use 1/4 sec shutter was a requirement, you would've need to manually block or add more light using ND filters or raising the ISO (or using flash) respectively, based on the ambient light conditions.
Do you ever shoot in manual mode, or always use shutter or aperture priority?