A Met Office yellow weather warning for rain was in place until midnight on Friday.
Brackaghlislea Road in Draperstown was closed at around midday. It is not expected to open until Saturday afternoon.
Water from adjacent land spilled out onto the road resulted in the drainage being overwhelmed, the Roads Service explained.
The Draperstown area of Co Londonderry has experienced significant rainfall with a number of roads experiencing flooding. They are passable with care.
In Co Down, Lisbane Road in Kircubbin has been closed due to severe flooding.