Stony Brook is a major watercourse, now almost entirely covered, in the city of Boston, USA. It runs through a culvert for 7.5 miles, along almost its entire length; despite being underground, it is the largest tributary stream of the lower Charles River.  It originates at Turtle Pond in the Stony Brook Reservation; it flows through Hyde Park, Roslindale, Jamaica Plain, and Roxbury. It empties into the Charles River Basin just upstream of the Massachusetts Avenue bridge; it formerly emptied into the Back Bay when that was a tidal estuary of the Charles River.
In the 18th century, water-powered industry grew up along it (including Pierpoint('s) Mill ) and it served as the sewer (excluding human waste) for the neighborhoods it ran through.
In the 19th century, many breweries and other industries grew up along Stony Brook. 
In the late 19th century, various parts of Stony Brook were converted into underground culverts or sewers. In around 1882, the Back Bay Fens were dredged to convert them into a holding basin for storm overflow from Stony Brook, following Olmsted's plan, and at around the same time its waters were diverted into an intercepting sewer near the current Ruggles Station.
- Weiskel, Peter K.; Barlow, Lora K.; Smieszek, Tomas W. "Water Resources and the Urban Environment, Lower Charles River Watershed, Massachusetts, 1630–2005". CIR 1280, Water Resources and the Urban Environment, Lower Charles River Watershed, Massachusetts, 1630–2005. US Geological Survey, US Department of the Interior. Retrieved 2 September 2017.
- "Boston, its environs and harbour, with the rebels works raised against that town in 1775, from the observations of Lieut. Page of His Majesty's Corps of Engineers, and from those of other gentlemen" 
- "Stony Brook", Heart of the City Project, Center for Urban and Regional Policy, Northeastern University, a database of greenspaces in Boston: http://ksgaccman.harvard.edu/hotc/DisplayPlace.asp?id=11378
- Weiskel, Peter K.; Barlow, Lora K.; Smieszek, Tomas W. "Water Resources and the Urban Environment, Lower Charles River Watershed, Massachusetts, 1630–2005": U.S. Geological Survey Circular 1280, 46 pages. CIR 1280, Water Resources and the Urban Environment, Lower Charles River Watershed, Massachusetts, 1630–2005. Retrieved 2 September 2017.
- "Annual Report of the Street Department", February 1, 1892 in Documents of the City of Boston for the Year 1892, 2:110 at Google Books
- Alex Krieger, David A. Cobb, and Amy Turner, Mapping Boston, p. 131ff
- "A Sewer Runs Through It", The City Record and Boston News-Letter, blog page
- "The Stony Brook During a Flood, c. 1890", The City Record and Boston News-Letter, blog page
- Edwin Munroe Bacon, Walks and rides in the country round about Boston full text
- W.H. Marx, "The Saga of Stony Brook", Jamaica Plain Historical Society http://www.jphs.org/locales/2004/1/5/the-saga-of-stony-brook.html
- A blog devoted to Stony Brook: http://stonybrookinboston.blogspot.com/
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