Houghton is a city in Lee County, Iowa, United States. The population was 141 at the 2020 census. It is part of the Fort Madison-Keokuk Microp…Houghton is a city in Lee County, Iowa, United States. The population was 141 at the 2020 census. It is part of the Fort Madison-Keokuk Micropolitan Statistical Area. Houghton is located at 40°46′59″N 91°36′45″W / 40.78306°N 91.61250°W.