Clearing muddy farm pond water means first identifying the cause. Muddy water can come from animals or shoreline erosion causing soil to filter into the pond, aquatic life stirring up the water, or water chemistry with a clay suspension. To learn the cause, use a clean gallon jar, fill it with pond water, write the date on it, and then set it aside to see how fast the mud settles. If the water clears in a week or less, the problem is most likely animals, aquatic life, or shoreline erosion. To correct these issues, you may need to remove aquatic life that is stirring up the pond or put measures into place to prevent shoreline erosion from the elements and animal traffic.
If the water takes longer to clear, it may be that there are suspended clay particles in the water. Spreading bales of barley straw or high-quality hay in the water near to the shore can help correct this. As the hay or straw breaks down, acids from the decay process can cause clay to settle.