All other things being equal, clear water ponds can produce many more fish than muddy ponds. Muddy water reduces fish food availability, and interferes with the ability of fish to see and catch prey. Muddy waters favor blue-green algae and bacterial growth, which can impart a bad flavor to drinking water and food fish. Green water is usually the result of algae, which is another type of problem with a different solution than that discussed here. It is a sad irony that the same soil that is vital for agricultural production on land becomes a major pollutant when suspended in water.
Muddy ponds are normally the result of soil erosion.
Heavy rains and strong winds transport eroded soil into ponds from over-grazed pastures, unprotected croplands, and bare shorelands. Any area of bare soil provides a source for soil erosion. Livestock trampling shorelands and wading in ponds or upstream waters add large quantities of soil and undesirable manure. Bottom-feeding fish, especially carp and bullheads, can contribute to muddy waters by rooting and stirring up bottom silt in their search for food. Prevention of soil erosion is the best way to keep pond water clear.