The bedrock of the eastern and western watersheds of Tuen Mun River is fine-grained granite, forming peaks such as Castle Peak and Kau Keng Shan. As granite in most areas in the eastern river basin is weathered and eroded, and large-scale deforestation in the area has also caused severe soil erosion, the ridges are generally flat and rounded and there are many badland features such as rills and gullies on the ridges and slopes
Tuen Mun Valley lies on the Tuen Mun – Lo Wu Fault Zone. Most of the bedrock of Tuen Mun Valley is andesite, forming low and round hills such as Por Lo Shan. Metamorphic rocks that originated from sedimentary rocks such as metasiltsand, metasandstone and phyllite occur to the northeast of the Tuen Mun Valley, stretching from Tuen Mun Treatment Works to Fuk Hang Tsuen. Sedimentary rocks such as sandstone, mudstone and conglomerate occur to the southwest of the valley at Tsing Shan Tsuen. Weathering and river erosion create concave slopes with large gradients forming dendritic drainage patterns, such as Tsz Tin Hang, and steep, narrow and convex ridges
The banks of Tuen Mun River Channel, from Tuen Mun Park to Tuen Mun Typhoon Shelter, originally belonged to the deeply indented bay of Castle Peak Bay. The riverbanks were reclaimed from the sea. The natural estuary lay between the present Pui To Road and Hau Kok Tin Hau Temple. There is no large alluvial plain along the lower course of Tuen Mun River; the main plains are at Fu Tei Ha Tsuen, San Hing Tsuen, Tsz Tin Tsuen and Kei Lun Wai. The colluvium is distributed on two sides of Tuen Mun Valley: eastern slopes of Castle Peak range and the northern river basin.