The city of Chicago is located in northern Illinois, United States, at the south western tip of Lake Michigan. It sits on the Saint Lawrence Seaway continental divide at the site of the Chicago Portage, an ancient trade route connecting the Mississippi River and the Great Lakes watersheds.

Chicago's present natural geography is a result of the large glaciers of the Ice Age, namely the Wisconsinan Glaciation that carved out the modern basin of Lake Michigan (which formed from the glacier's meltwater). The city of Chicago itself sits on the Chicago Plain, a flat plain that was once the bottom of ancestral Lake Chicago. This plain has very little topographical relief; in fact, topographical relief is so unusual in the plain that what would be unnoticed hills and ridges in other locales have been given names. The highest natural point within the city limits is in the Beverly neighborhood at 41°42′12.5″N 87°40′37″W / 41.703472°N 87.67694°W / 41.703472; -87.67694 at 672 ft (205 m). In pioneer days, this hill was called Blue Island, so named because at a distance it looked like an island set in a trackless prairie sea. In fact, it and the nearby Stony Island were both islands in Lake Chicago as it receded. On the North side, the diagonals Clark Street and Ridge Boulevard run along ridges that were once sandbars in the Lake.

One special feature of the Chicago area was the now-vanished Mud Lake in the Des Plaines River watershed. During heavy periods of rain or when the Des Plaines overflowed its banks due to downstream ice dams in the early spring, the river would flow through Mud Lake to the South Branch of the Chicago River, forming a favorite portage for early traders and creating the path of the future I&M and Chicago Sanitary and Ship Canals. When the city we know today was initially founded in the 1830s, the land was swampy and most of the early building began on low dunes around the Chicago River's mouth. Indeed, Chicago's low lying geography, which ultimately became crucial to its boom town development (as the site of the Chicago Portage and canal), could not initially attract substantial early settlement because the tall grass prairie around its lake and river systems was underlain by hard packed glacial clay, making much of the area forbidding wetlands. Thus, the paradox of Chicago's development as a city in the 19th century became taking advantage of this geography, but also overcoming its limitations.

North of the city of Chicago, there are steep bluffs and ravines that run along Lake Michigan. In contrast, south of the city of Chicago into Northwest Indiana it is without bluffs, but instead has sand dunes. The greatest example of these can be seen at Indiana Dunes National Park, where some dunes reach up to almost 200 feet. Farther inland, a series of moraines surrounds the Chicago Plain. This surrounding area is hilly and higher than the Chicago Plain. Past the moraines, the land flattens out again, but is interspersed with a few deep river valleys such as the Illinois River, Fox River, Des Plaines River, and Kankakee River. Here you may find rock cliffs and rock ravines, which are absent from the interior Chicago area (the ravines of the north shore and south suburbs are soil ravines without any rock).

During the Silurian geological age, the area now known as Chicago was submersed under a warm saltwater sea. Limestone eventually formed from the decay and buildup of shellfish and other calcium-rich sea creatures. In the Chicago area, the limestone underwent a further transformation into dolostone. Dolostone is the bedrock beneath Chicago's dense layer of clay and glacial debris.

The world's second largest aggregate quarry, Thornton Quarry, exists just south of the city limits in the suburb of Thornton. The dolostone bedrock rises close to the ground surface in this area, and hence this area has had active quarries since the 1840s.

This layer of ancient Silurian dolomite is usually hundreds of feet below the ground surface throughout much of the Chicago area. Exceptions include near the Stearns Quarry in the Bridgeport neighborhood, the quarry (now landfill) in Hillside, the lower Des Plaines River and the Calumet-Sag Valleys. The Silurian dolostone bedrock is also exposed at the ground surface when the Kennedy Expressway dips below the UP Northwest Line near Addison Street.

The city lies within the humid continental climate zone, and experiences four distinct seasons. Summers are warm and humid with a July average of 75.5 °F (24.2 °C). Winters are cold, snowy and windy with temperatures below freezing. Spring and fall are mild with moderate humidity. According to the National Weather Service, Chicago's highest official temperature reading of 107 °F (42 °C) was recorded on June 1, 1934. The lowest temperature of −27 °F (−33 °C) was recorded on January 20, 1985. Along with long, hot dry spells in the summer, Chicago can suffer extreme winter cold spells. In the entire month of January 1977, the temperature did not rise above 31 °F (−0.6 °C). The average temperature that month was around 10 °F (−12 °C).