The route runs through Niles Canyon, parallel to the Niles Canyon Railway, Highway 84, and the Hetch Hetchy Aqueduct. The line passes through a long tunnel which cuts off one of the canyon's horseshoes. This tunnel was modified from its original configuration to accommodate intermodal double-stack freight trains. However, this left the track in poor condition, reducing speeds from to in the summer and as low as during the rainy season. The San Joaquin Regional Rail Commission plans to rehabilitate the tunnel.