You need to get that crap out of the pond. Do you have a rock bottom? And in the intrim clean your filters more regularly as it filters out what is being stirred up. Daily if you need to.

Its a liner with some rocks at the bottom, although not intentionaly. I can never seem to get rid of all of them.

If the fish are stirring up stuff, odds are it's in need of a good serious cleaning.

Although that come's with some hazards as some nasties (bacterial) can be released when you scoop the stuff out.

Use a good net, and try to scrape it along the bottom to get the stuff out.

And make sure to clean your filters as you go. They will trap the stuff that floats around.