At least 20 roads in the county are closed, as flooding continues to affect parts of Northern Ireland in the wake of Storm Desmond at the weekend.
The Rivers Agency said prolonged rainfall meant saturated ground and high water levels in lakes and rivers.
Its chief executive, David Porter, said they were monitoring the situation.
"Rivers Agency and the Electricity Supply Board (ESB) in the south are responsible for controlling the lough levels and we are working closely to ensure everything can be done to reduce the levels and therefore the impact of any flooding," he said.
"A combination of generation and spilling at the hydroelectric power stations at Cliff and Ballyshannon in Donegal is ongoing to ensure that water can leave the Erne system as quickly as it can flow down to the dams.
"It should, however, be recognised that heavy rain can result in a greater inflow than can possibly be dealt with, even when spilling is in progress."
He said the River Blackwater, which flows through counties Armagh and Tyrone, was at its "highest recorded level in 45 years but has now peaked".
In County Armagh, firefighters rescued a man from a van that was trapped in flood water.
It happened in the Armagh Road area of Charlemont at about 08:00 GMT on Wednesday. The man was not injured.
Some businesses have also been affected by the flooding.
Tom Leonard, who is the owner of a marina at Carrybridge, County Fermanagh, said water levels were within "seven to eight inches" of what they were in 2009.
"It has left us now today that we are trying to salvage the customers' boats and protect them," he said.
"At the moment, after this week then we have to lay off all the lads until after Christmas which annoys me more than anything else.
"They have been with us all summer and now we have to lay them off in the mouth of Christmas because we just don't have a workshop to work in and we have lost all our stock."
Further flooding in County Fermanagh is possible as heavy rain continues to raise water levels at Upper Lough Erne, the Rivers Agency has warned.