Situated on the Kanto Plain, Tokyo is one of three large cities, the other two being Yokohama and Kawasaki, located along the northwestern shore of Tokyo Bay, an inlet of the Pacific Ocean on east-central Honshu, the largest of the islands of Japan. The central part of the city was once marsh and lagoons that were filled in when Ieyasu took over. This area is called shitamachi, or "low city," site of the original Edo. The terrain becomes increasingly hilly to the west of the city's center until it becomes the Musashino Plateau, where Yoyogi Park, the Meiji Shrine, Roppongi, and fashionable Harajuku are located. Other notable places on the west side are the nightclub district of Roppongi and the high-fashion districts of Aoyama and Harajuku.

Tokyo is intersected by the Sumida River and has an extensive network of canals. There is a large man-made port at the mouth of the Sumida, the development of which has enabled Tokyo to compete with Yokohama, the area's foremost port. Land reclamation projects have added to Tokyo's available surface area by filling in the bay and providing room for waste disposal, additional port facilities, and new residential areas.

Pollution of the environment is regarded as a matter of public offense. While the national government is often slow to address environmental issues, growing public pressure has led to legislation requiring industrial polluters to rectify any environmental damage for which they are responsible. In spite of widespread use of bicycles and public transportation, automobile exhaust is a problem in Tokyo. The imposition of emission standards has lately eliminated some of the smog that has plagued the city.