In really dirty water you just can't avoid lighting up the stuff in the water. What you can do is make it blend in to the lighter background. Shoot up towards the surface and play with shutter speed for more or less ambient exposure.
More likely there is something wrong with your version of Photoshop or operating system. Can you open the Photoshop file in someone else's Photoshop? Resize an offending image to Email able size and I'll check it on mine if you want. apnewton at gmail etc