In Northern Ireland the county borders County Tyrone to the north-east, and in the Republic of Ireland the county borders County Monaghan to the south-east, County Cavan and County Leitrim to the south-west and County Donegal to the north-west. Fermanagh is the only county of Northern Ireland that does not border Lough Neagh.

County Fermanagh is a predominantly rural region with its geography dominated by two lakes: Upper Lough Erne and Lower Lough Erne. This 70-km (40 mi) stretch of lakes, known collectively as Lough Erne, is now linked to the River Shannon and its waterways via the Shannon-Erne Waterway canal, making the entire system the longest navigable inland waterway in Europe. Smaller lakes in the county include Lough Scolborn. In addition, Fermanagh shares many lakes: Lough Melvin (with the Republic of Ireland), Lough Macnean Upper and Lough Macnean Lower (both lying on the Cavan border).

There are also a large number of small rivers running through Fermanagh, generally these will enter the Erne system. Some notable examples are the Arney River, Sillees River, Owenbrean River, Cladagh River, Sruh Croppa, Aghinrawn and the Colebrook River.

The peak of Cuilcagh, part of the Cuilcagh Mountains range, on the Fermanagh/Cavan border is the highest point in Fermanagh (665 metres, 2,182 feet). Other mountains/ranges include Belmore Mountain, Tappghan Mountain (on the border with Tyrone), Brougher Mountain (on the border with Tyrone), Molly Mountain, Benaughlin Mountain, Slieve Rushen (on the border with Cavan), Derrin Mountain and Slieve Beagh (on the Tyrone border). Much of the western and eastern areas of the county are forested.

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