There is an actual Stony Brook which flows from Turtle Pond in Hyde Park to meet the Muddy River through the valley you are standing in. Today the Stony Brook still flows into the Muddy River. This location is on the Riverway near the Museum of Fine Arts and is marked by two headhouses - one of which houses a Visitors Center for the Emerald Necklace Conservancy.
We assume the indigenous inhabitants took advantage of this waterway since some fish hooks were discovered by archaeologists along the Southwest Corridor Park. During the first few centuries of European settlement, the Stony Brook provided water for agriculture uses. But as Jamaica Plain and neighboring Roxbury industrialized the unpredictability of the Brook (spring flooding caused by snow melt called a freshet) caused the Brook to be banked with stone walls by the 1860s to better control it.
Eventually, the Boston Water and Sewer Commission put the Stony Brook into an underground culvert during the 1880s, completing the work through Roxbury by the early twentieth century. However, there remains an easement that no buildings can be built over the Stony Brook - so if you use Google Earth you can easily plot its path. Will point out a place to see this along the tour route too.