I have the same problem as well when shooting salmon in streams using ambient light. There is a fair amount of drifting debris. Bubbles can be a problem (as just suggested) as well. Shooting with a fisheye lens at point blank range helps to minimize the problem. As well, it is best to avoid shooting into the light. Sometimes one does not much of a choice other than not shooting at all.
Check out this shot:
(easier for me to find image on my site). Note the light blotches in the water column. I see a dark one too (left side), probably a twig. Not too bad backscatterwise at the spawners that were real close. I angled the camera to avoid shooting into the sun - this gave the reverse perspective from many of my other shots - but easy to see the eggs emerging from the female from this angle! A downside is that the housing cast a shadow on the bottom (shot taken less than 2 hours from true noon).
- bmorescuba likes this