The Mystic River Watershed has an area of approximately 76 square miles, encompassing 21 communities north and west of Boston, Massachusetts. The headwaters of the system begin in Reading and form the Aberjona River, which flows into the Upper Mystic Lake in Winchester. The Mystic River flows from the Lower Mystic Lake through Arlington, Medford, Somerville, Everett, Charlestown, Chelsea, and East Boston before emptying into the Boston Harbor. Main tributaries to the Mystic River include Mill Brook, Alewife Brook, Malden River, and Chelsea Creek. The watershed contains 44 lakes and ponds, the largest of which is Spot Pond in the Middlesex Fells, with an area of 307 acres.

Home to about 8% of the state's population (more than half a million people) in less than 1% of its land area, the Mystic is one of the most densely populated and urban watersheds in Massachusetts. Eight out of the fifteen Massachusetts communities "most intensively overburdened" by cumulative environmental hazards lie within this watershed, according to recent environmental justice research.