The county was formed in 1792. In 1845, the southern portion of Lincoln County was separated to form Welland County.
In some census and election records from the late 1800s, the townships of Caistor and Gainsborough (which can be seen on the map below) were enumerated as part of Monck County, while Grantham and Niagara Townships were enumerated as part of Niagara County. However, neither Monck nor Niagara ever existed as incorporated municipal counties, but rather as an electoral district.
In 1970, Lincoln and Welland Counties were amalgamated to form the Regional Municipality of Niagara.