The causes for brown and cloudy water may include rust in the piping, other iron-related problems, surface infiltration and well-structure problems. A proper diagnosis requires testing the water at a lab, which should be done before a plumber is called.
Rust is generally the cause of the problem when only the hot water is discolored. Rust can also be responsible if both the hot and cold pipes have brown water, but this usually happens when only one plumbing fixture in the house has the problem. When the water supply is shut down and turned back on, it is common for rust in the plumbing to dislodge and make the water brown. Other causes for iron in the water include water seepage from rainfall and steel well-casing corrosion.
Flooding, excessive rain or snow melt can also cause brown and cloudy water due to surface infiltration. These events cause problems if the well cap is not sealed properly or is damaged. Testing the well for coliform and fecal coliform bacteria can indicate surface infiltration because damage to the well surface can allow these types of bacteria to enter it.
A problem with the well structure or water level can also be responsible for brown water in the well. The well pump may pull up mud or could be hitting the side of a well hole, which happens when there are changes in water supply or level.