Shing Mun River flows through the central New Territories, to the southeast of Tai Mo Shan, and originates from peak of the 957m mountain, at an altitude of 930m – making it the highest source of any Hong Kong river. The highest section of main stream of Shing Mun River, named Tai Shing Stream, flows northeast and then turns southeast into Shing Mun Reservoir. The stream flows southeast and enters Lower Shing Mun Reservoir. Passing the main dam of the lower reservoir, the stream zig-zags northeast through Tai Wai, and enters Shing Mun River Channel. Converging with Kwun Yam Shan Stream, Siu Lek Yuen Nullah and Fo Tan Nullah, the river enters Tide Cove at Shatin Sewage Treatment Works. The estuary of the original Shing Mun River is at Hong Kong Heritage Museum. The channel north of the museum was artificially reclaimed from the shallow sea, and is now Shing Mun River Channel.
The basin of Shing Mun River is divided into upper and lower sections by Needle Hill. The upper basin, Shing Mun Valley, rises to near the summit of Tai Mo Shan. To the west is the ridge leading from Tai Mo Shan to Pineapple Pass Dam, to the north is Sze Fong Shan and Grassy Hill, and Needle Hill ridge lies to the east. The lower basin is named Sha Tin Valley. To the north is a ridge extending eastward from Grassy Hill, to the northwest is Needle Hill ridge above Shing Mun Valley, and to the southwest is Smugglers' Ridge. The south side is bordered by a range of mountains: Beacon Hill, Lion Rock, Tsz Wan Shan, and Tate's Cairn, while to the east are Tung Yeung Shan, Buffalo Hill and Nui Po Shan.
The various streams originating from the headwater at Tai Mo Shan flow in different directions, and form a typical radial drainage pattern. The main stream converges with other tributaries in Shing Mun Valley, and enters Shing Mun Reservoir, creating a dendritic drainage pattern. Sha Tin Valley, on the other hand, has a rectangular drainage pattern, formed by around twenty tributaries flowing parallel from the north and south of the valley, and entering the main stream at almost a right angle. The main stream of Shing Mun River is 16.5km long, horizontally; and has an average gradient of 0.056 (or 1:17.7). The river basin area is about 58km.