According to SFGate, pond water turns brown for a number of reasons, but the most common causes are eroding soil, microscopic plants and wildlife. High amounts of microscopic plants such as algae and phytoplankton give pond water an almost tea-like look. Soil erosion causes the banks of the pond to break away and fall into the water, giving it a brown look.
SFGate says that the rapid growth of algae, known as algal blooms, are caused by high amounts of animal waste, nitrogen and phosphorous in the pond water. When this happens, the pond water starts to turn green. However, as the algae starts to decompose, the water starts turning brown. The breakdown of any kind of organic material in a pond causes brown water. One example of this organic material is falling leaves from nearby trees.
There is a variety of ways to prevent brown pond water. For example, planting vegetation around the banks of the pond creates a buffer zone. This eliminates foot traffic close to the edge of the pond, preventing soil erosion. It is also possible to keep the fish population down in a pond by stocking it with predatory fish such as the largemouth bass.