Muddy Run is a 6.61-mile-long (10.64 km) stream in northern New Castle County, Delaware in the United States.

Muddy Run rises on the Persimmon Run divide in New Castle County, Delaware and flows south then northeast to meet the Christina River at Heather Woods.

Muddy Run drains 14.95 square miles (38.7 km2) of area, receives about 45.6 in/year of precipitation, has a topographic wetness index of 581.51 and is about 23.1% forested.

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