Khor Kharfot is part of a coastal estuarine wetland system located in the western part of the Dhofar Governorate preserving a pristine ecosystem supporting a distinct vegetation and animal habitat. A sand barrier along the khor (local term for wetlands) mouth controls the mixing of fresh and marine water in the enclosed lagoon. In order to understand the geological controls on the khor formation, a geological map of the khor barrier and inlet area is prepared. The khor is bounded by Cretaceous and Tertiary carbonate rock sequences which are cut by a number of faults. The khor mouth and barrier are comprised of late Holocene deposits divided into seven units including i) beach sand, ii) beach sand mixed with wadi gravels, iii) scree and coastal dunes, iv) lagoon, v) soil and boulders, vi) wadi gravels, and vii) talus. The khor developed as an open estuary which changed to a barrier dominated lagoon due to falling fresh water supplies as a consequence of dwindling Khareef rains. The lagoon water is brackish due to the mixing of fresh and marine water and supports a distinct flora and fauna.