Mike, I believe that the presence of alligators in your pond is not the cause of your muddy water. If you watch them you'll see that they just float around waiting for opportunities to ambush food items. The three footers are relatively inocuous but the seven footers would probably, and the twelve footer would absolutely, consider pets, children and even adults to be on the menu. I urge you to contact your Department of Wildlife and or Fisheries to have the alligators removed. If they are unresponsive, consider removing them yourself.