Kochi is located on the southwest coast of India at 9°58'N, 76°13'E, spanning an area of 94.88 ;square kilometres (36.63 sq mi). The city is situated at the northern end of a peninsula, about 19 kilometres (12 mi) long and less than one mile (1.6 km) wide. To the west lies the Arabian Sea, and to the east are estuaries drained by perennial rivers originating in the Western Ghats. Much of Kochi lies at sea level, with a coastline of 48 km.

The current metropolitan limits of Kochi include the mainland Ernakulam, old Kochi, the suburbs of Edapally, Kalamassery and Kakkanad to the northeast; Tripunithura to the south east; and a group of islands closely scattered in the Vembanad Lake. Most of these islands are very small, varying in extent from six square kilometre to less than a square kilometre (1,500 to less than 250 acres).

Soil consists of sediments such as alluvium, teri's, brown sands etc. Hydromorphic saline soils are also found in the areas surrounding the backwaters. Predominant rock types found here are Archaean-basic dykes, Charnockites and Gneisses. An ecologically sensitive area, the Mangalavanam Bird Sanctuary is located in the central part of the city. It has a wide range of mangrove species and is nesting ground for a vast variety of migratory birds. Certain species of dolphins are also present in the backwaters.

Kochi's proximity to the equator along with its coastal location results in little seasonal temperature variation, with moderate to high levels of humidity. Annual temperatures range between 20 to 35 °C (68–95 °F) with the record high being 38 °C (100 °F), and record low 17 °C (63 °F). From June through September, the south-west monsoon brings in heavy rains as Kochi lies on the windward side of the Western Ghats. From October to December, Kochi receives light rain from the northwest monsoon, as it lies on the leeward side. Average annual rainfall is 3,500 millimetres (138 in), with an annual average of 132 rainy days.