Muddy water in a farm pond is a problem for many people who own them. Water that is muddy isn't aesthetically pleasing and can hurt wildlife in the pond. When the water is muddy, particles of silt block sunlight from penetrating the water and providing the energy needed for the initial step of photosynthesis. It is through photosynthesis that phytoplankton (the microscopic plants at the bottom of the food chain) are created, supplying a source of food for fish and other wildlife in the pond. There are ways you can clear the pond water, though.
Stop any soil erosion into the pond. If there are any bare areas around the shoreline of the pond, lay sod to stop dirt from running into the pond when it rains.
Scoop a bucket of water out of the pond and check it two or three days later. If the water is clear, that could mean that the sediment on the bottom of the pond is getting stirred up by large fish such as carp or bullheads. Try fishing the pond with dough balls or catfish bait to find out whether large fish are in your pond. If they are, catch the fish and transport them to another body of water to be released. Note: Check with your state's environmental agency to make sure you can release these fish into a different body of water, and to make sure that they're not a an invasive species that could harm the environment.
If the water is still muddy, check for negatively charged clay particles. These particles cause a muddy appearance because they repel each other and never settle to the bottom. Check the pH levels of the pond with a water-testing kit. The pH should be between 6.5 and 9, and the alkalinity should be at least 20 parts per million; if these numbers aren't met, add lime to the pond to reach them. Your state's agriculture department or department of environmental protection can give you guidance.
Apply gypsum or aluminum sulfate (alum). Get six gallon-size containers made of glass or another clear material and use them to take samples of the pond water. You will leave one of the containers untouched as a control sample. Mix 2 tbsp. of gypsum in a gallon of clear water, stirring it around until you get a slurry mix.
Put the gypsum slurry in four of the jars containing the pond water. Put 1 tbsp. in the first jar, 2 in the second jar, 3 in the third jar, and 4 in the fourth jar (labeling each jar so that you know how much gypsum was applied).
Check the results in about 12 hours. If the water is still not clear, empty out and wash the jars, and take four more samples. Put the gypsum mix into the new samples, but this time, use 5 tbsp. in the first jar, 6 in the second jar, 7 in the third jar, and 8 in the fourth jar. Check the results in 12 hours.
When the water in a jar has been cleared by the gypsum, see how many tablespoons of the slurry it took to clear the water. To figure out how much gypsum you'll need to add to the pond to clear it, multiply the number of tablespoons by 80. This will tell you the number of pounds of gypsum per acre-foot of pond water needed to clear the pond. Use the lowest level of gypsum needed to clear the pond.
If using alum instead, you'll follow the same process to determine how much alum is needed that you did to determine how much gypsum would be needed, only you'd multiply the number of tablespoons used in the sample by 30 (instead of 80 as with the gypsum) to determine how much alum is needed. Again, use the lowest amount of alum needed to clear the pond.