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In 1837, most of the area of present-day Brazos County was included in Washington County. The Brazos River, which bisected the latter, proved a serious obstacle to county government, and a new county, Navasota, was formed in January 1841. The first court, with Judge R. E. B. Baylor presiding, was held later that year in the home of Joseph Ferguson, fourteen miles west of the site of present Bryan. The county seat, named Boonville for Mordecai Boon, was located on John Austin's league and was surveyed by Hiram Hanover in 1841. In January of the following year Navasota County was renamed Brazos County.

Originally one of the state's poorer counties, the county donated 2,416 acres of land in the 1870s to create Texas A&M University, which has enabled the county to be among the state's most financially successful.

After the Civil War tens of thousands of new residents moved to Brazos County, attracted by its good lands, with plenty of timber and a patchwork of prairies and fertile floodplains. As newcomers poured in by the thousands the county suffered from arson, feuding, shooting and racial violence, including mob lynchings.