It is uncertain when they adopted the "Niwa" surname, but during the Muromachi period were in service of the Shiba clan, who were the shugo of Owari Province.

However, Toyotomi Hideyoshi was mercurial in his moods, and in response to Niwa Nagashige's efforts at the Siege of Odawara, his status was brought back to 120,000 koku.

During the Boshin War, Niwa Nagakuni joined the Ōuetsu Reppan Dōmei in 1868; however, his forces were defeated by the Satchō Alliance and Nihonmatsu Castle was burned.

The victorious Meiji government reduced the domain to 50,700 koku under the final daimyō Niwa Nagahiro, who subsequently served as imperial governor until the abolition of the han system in 1871.

Another clan, the Isshiki-Niwa, who were daimyō of Mikusa Domain (10,000 koku) in Harima Province from 1746 to 1871, bears the same Niwa but is not directly related to the above.