As of 2011, a total of of streams in the watershed of Mud Creek were affected by
organic enrichment, low concentrations of
dissolved oxygen, and heavy loads of
sediment. The entirety of every stream in the creek's watershed was considered by the
Pennsylvania Department of Environmental Protection to be impaired as of 2011. The daily load of sediment in Mud Creek was as of 2011, but the
total maximum daily load, above which water quality is considered impaired, is only . The largest contributor of sediment to the creek was
cropland, which contributed per day. of sediment per day came from
stream banks and came from hay and pastures. came from land classified by the Pennsylvania Department of Environmental Protection as "transition", per day came from forest, and from land classified by the Pennsylvania Department of Environmental Protection as "low-intensity development". came from
wetlands. Many of the streams in the watershed can be
muddy for a number of days after
thunderstorms. As of 2011, the load of
phosphorus in Mud Creek was per day, but the total maximum daily load is . per day came from cropland, from
groundwater, and from hay and pastures. An average of per day of phosphorus came from land classified by the Pennsylvania Department of Environmental Protection as "transition". came from forest, from land classified by the Pennsylvania Department of Environmental Protection as "low-intensity development", and from stream banks.
Septic systems contributed of phosphorus per day to the creek and wetlands contributed . ==Geography, geology, and climate==