The city lay on a tapestry of islands, lagoons, and creeks interspersed by mangrove. Much of its land surface is barely above sea level; since 1989, parts of Victoria Island had been under threat from a rising tide. Land has been reclaimed to build a road on the Marina, as well as make the Five Cowries Island more functional; the flyovers between Ìkòyí and the island also stand on once-swampy terrain.

Air pollution is endemic. Local historian Kunle Akinsemoyin has remarked that in present-day Lagos, "walking is … a dangerous hazard, cycling a perilous venture, for the motor car, particularly the lorries have grabbed the monopoly of roads from the cyclists." This reflects several factors,

Street markets are popular in Lagos. Here, a vendor takes a rest from the busy shopping day. ()
including overpopulation, weak physical planning enforcement, and emissions by vehicles and industrial plants. Sewage disposal has been long problematic. The Lagos lagoon has long served as dump for refuse and untreated sewage; it is thus extremely polluted.

Greater Lagos is bordered to the east, west, and north by other towns in Lagos State. Of the 3,577 square kilometers (1,381 square miles) land surface in Lagos State, lagoons constitute about 790 square kilometers (305 square miles) or 22 percent of the total. Much of the state's land surface is just over five meters (15 feet) above sea level.