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Waterloo's history dates back to the 1780's, when settlers formed the first permanent American settlement in the entire Northwest Territory-Bellfontaine, named for the beautiful spring that served as stopping place for the French traveling between the two French settlements of Cahokia and Kaskaskia.

The area grew to such an extent that by 1800, the population of Bellfontaine had reached 286.

In 1816, a man named Emery Peters Rogers arrived in the area and, four years later, opened the first permanent store, mill, and quarry. The neighborhood around his store soon came to be known by his name- Peterstown.

As the years passed, the town was divided into two parts Bellfontaine at the south and Peterstown at the north. The two communities were divided by a creek, and there was said to have been intense rivalry between them.

Legend has it that in 1818, a man named Charles Carroll, an Irishman, came upon the scene, and to the astonishment of the Peterstown men and the Bellfontainers, ignored the rivalry and built his house on one side of the creek, his barn on the other and said "It won't be Bellfontaine, and it won't be Peterstown, but begorra, I'll give ye's both your Waterloo."

The town experienced a marked population increase in the 1840's, and that is when the German population got its impetus. Many of the city's buildings and its citizens today still reflect the heritage left by those German settlers.

Waterloo received its charter as a town February 12, 1849, and the charter was amended in 1857 and 1859. It was chartered as a city on August 29, 1888.

Waterloo became the Monroe County seat in 1825. On December 1, 1978, it's historic district was recognized and placed on the National Register of Historic Places.

The City of Waterloo also has been recognized for its work through Sister Cities International. In 1980, Waterloo formed a Sister Cities partnership with Porta Westfalica, West Germany, and has been since been honored with six coveted Reader Digest awards for it's Sister Cities program. Every summer this city holds it annual "Porta Westfalica Fest" In honor of its Sister City.