The McIntosh Run River flows within the Halifax Regional Municipality on the Atlantic coast of Nova Scotia. About 13 kilometres of river feed into Long Lake. The river flows through the community of Spryfield and into the “Backlands” (between Herring Cove and Purcells Cove roads) where it connects to ponds and wetlands. The McIntosh Run then drains into the Atlantic Ocean through Herring Cove.
Human-built infrastructure that connects Long Lake to Spruce Lake and other lakes in the Chain of Lakes System has increased the area of the McIntosh Run watershed beyond its natural topographic boundaries. The watershed area is about 37 square kilometres. Natural vegetation includes spruce-pine-fir forests, pine/crowberry granite barrens, and a mosaic of wetlands and lakes. About half of the land is private, and half is provincial Crown land.

About 17 000 people live in the watershed. The growing population puts pressure on the ecological health of the Run, though changes in water discharge, past effluent contamination, acid-rock drainage contamination, and habitat alteration.