When faced with a muddy pond, the first thing a landowner must do is to evaluate the area around and up-slope from the pond. If the area around the water's edge is devoid of vegetation because of animal traffic (i.e. cattle or other livestock drinking from the pond) that can be the culprit. Bare soil in pastures, and runoff water from construction and other disturbed areas can also be to blame.
Fixing bare areas that are in your control or waiting out nearby construction projects may be necessary before trying in earnest to get the water cleared up. Restricting livestock access to the pond via fencing and using a trough, or creating a designated watering pad in the pond may enable the shoreline to regrow vegetation and help clear the water up.
The muddy appearance of the water is typically the result of negatively charged, suspended clay particles in the water. Once you have taken care of the muddy runoff situation, you can focus your attention on trying to clear the water. Clearing the water will require changing the electrical charge on the clay particles, enabling them to sink.
The process of changing the clay particle charge involves testing the pond water's pH and alkalinity. If the alkalinity is below 20 parts per million, then the addition of up to 3 tons of agricultural limestone per surface acre might help the pond water clear up.
If adding the limestone does not help, then the landowner can run a few tests to determine if adding either gypsum or alum.
This publication describes the process of clearning muddy ponds in detail. muddypondstexas.pdf
