If you used the flash, they were probably translucent particles suspended in the water. It's called Backscatter and has to do with the flash being too near the lens so the particles reflect the light directly back onto your image. That's why most better camera setups move the flash(es) out to the side on an extension arm.
You can clean them up somewhat by using Photoshop/Photoshop Elements or a similar program using the clone tool to replace the bad areas. Or if they're uniform in color(typically red) try reducing the corresponding color channel/level slightly.
Post one so we can see the problem and give you other options.
Steve