Between 1834 and 1836, Brink and Follett surveyed the land to create the town of Mequon. Around this time, settlers came from New York and England, soon followed by German and Irish immigrants. In 1839, a group of immigrants from Saxony settled near the Milwaukee River. In the same year, twenty families from Pomerania founded Freistadt (German Free place) in western Mequon township. The first Lutheran church in Wisconsin was built by these families in 1840.
John Henry Thien, a wealthy immigrant from Saxony, travelled north from Milwaukee and settled along the Milwaukee River, where his family made a dam and grist mill. This area, one square mile in the middle of Mequon township, later was incorporated as the village of Thiensville in 1910.
The town of Mequon was incorporated as the City of Mequon in 1957.
According to the United States Census Bureau, the city has a total area of 46.8 square miles (121.3 km²), of which, 46.2 square miles (119.6 km²) of it is land and 0.6 square miles (1.6 km²) of it (1.35%) is water.
Mequon is the fifth-largest city in terms of land area in the state of Wisconsin.
In Mequon, the warmest month of the year is July, when the high temperature averages 78°F (25°C), with overnight low temperatures of approximately 58°F (15°C). July is also the wettest month of the year, with the majority of rain falling in short-lived thunderstorms. January is the coldest month in Mequon, with afternoon high temperature averaging only 26°F (-4°C), and overnight lows averaging 11°F (-12°C). February is the driest month, and almost all precipitation falls in the form of snow during that time. In an average winter, 47.0 in (1.3m) of snow falls. The city's proximity to Lake Michigan often increases the snow received by the city. Most of the city's snowfall comes from systems such as Alberta Clippers and Panhandle Hooks.
The highest temperature ever recorded in Mequon was 105°F (41°C) on July 24, 1935, and again on July 17, 1995. The coldest temperature ever recorded in the city was -40°F (-40°C), on January 17, 1982, also known as Cold Sunday.
There were 7,861 households out of which 38.0% had children under the age of 18 living with them, 74.8% were married couples living together, 4.8% had a female householder with no husband present, and 18.5% were non-families. 16.1% of all households were made up of individuals and 7.4% had someone living alone who was 65 years of age or older. The average household size was 2.75 and the average family size was 3.09.
In the city the population was spread out with 28.1% under the age of 18, 4.2% from 18 to 24, 22.9% from 25 to 44, 31.2% from 45 to 64, and 13.6% who were 65 years of age or older. The median age was 42 years. For every 100 females there were 97.4 males. For every 100 females age 18 and over, there were 93.8 males.
The median income for a household in the city was $90,733, and the median income for a family was $101,793. Males had a median income of $72,762 versus $40,280 for females. The per capita income for the city was $48,333. About 1.3% of families and 1.7% of the population were below the poverty line, including 1.2% of those under age 18 and 2.7% of those age 65 or over.