Wathena is a city in Doniphan County, Kansas, United States, located about 5 miles west of St. Joseph, Missouri. As of the 2020 census, th…Wathena is a city in Doniphan County, Kansas, United States, located about 5 miles west of St. Joseph, Missouri. As of the 2020 census, the population of the city was 1,246. Wathena was founded in 1856. The city is named in honor of Chief Wathena, a Native American chief of the Kickapoo tribe who previously lived in the area.