Deep Run may refer to the following places in the United States:

• Deep Run (Godbolt Creek), a tributary of the Godbolt Creek in Baldwin County

• Deep Run (Ellison Creek), a tributary of the Ellison Creek in Henderson County

• Deep Run, Maryland, an unincorporated community in Carroll County
• Deep Run (Big Pipe Creek), a tributary of Big Pipe Creek in Carroll County
• Deep Run (Fifteenmile Creek), a tributary of Fifteenmile Creek in Allegany County
• Deep Run (Jones Falls), a tributary of Jones Falls in Baltimore County
• Deep Run (North Branch Patapsco River), at tributary of the North Branch Patapsco River in Carroll County
• Deep Run (Patapsco River), a tributary of the Patapsco River

• Deep Run (Alloway Creek), a tributary of Alloway Creek in Salem County
• Deep Run (Great Egg Harbor River), a tributary of the Great Egg Harbor River in Atlantic County
• Deep Run (South River), a tributary of South River in Middlesex County
• Deep Run (Springers Brook), a tributary of Springers Brook in Burlington County

• Deep Run (Canandaigua Lake), a tributary of Canandaigua Lake in Ontario County

• Deep Run, North Carolina, an unincorporated community in Lenoir County
• Deep Run (Broad Creek), a tributary of Broad Creek in Beaufort County
• Deep Run (Dawson Creek), a tributary of Dawson Creek in Pamlico County
• Deep Run (Upper Broad Creek), a tributary of Upper Broad Creek in Craven County

• Deep Run (Tohickon Creek), a tributary of Tohickon Creek in Bucks County

• Deep Run Baptist Church, a historic church in Henrico County
• Deep Run Park, a public park in Henrico County

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