The Bureau of Meteorology on Sunday issued a warning for the Gwydir, Peel, Namoi, Hunter, Paterson and Williams river catchments.

A slow-moving low pressure trough will deepen later on Sunday or Monday, bringing heavy rain that is expected to linger over northeast NSW.

State Emergency Service Assistant Commissioner Sean Kearns said communities in the Hunter area and Tamworth, Narrabri, Coonamble and Coonabarabran in particular need to be ready.

"As heavy rain is very likely, flash and riverine flooding is a risk we need our communities to be aware of," he said.

Flooding is already occurring at Coutts Crossing, south of Grafton on the Orara River, but river levels are falling.

A warning for the Bellinger River at Thora, southwest of Coffs Harbour, has also been issued, with minor flooding expected to begin on Monday.

Severe thunderstorms are expected to bring heavy rainfall, damaging winds, flash flooding and large hailstones to the northeast corner of NSW.

Lismore, Tenterfield, Byron Bay, Ballina, Casino and Kyogle are in the firing line.

A severe weather warning has also been issued for Tamworth, Gunnedah, Narrabri, Walgett, Lightning Ridge, Scone, Coonabarabran Armidale and Maitland.

The Kimberley and northern interior regions of WA are also due to cop a lashing, with heavy rainfall and damaging winds.

The storms could cause significant damage to homes and property, the BOM has warned.

Massive rainfall totals have already been recorded, with Lombadina on the Dampier Peninsula receiving 244mm in a day - almost half of that falling in a single hour.

Locations that may be affected include Broome, Derby, Halls Creek, Kununurra, Wyndham, Kalumburu, Kuri Bay, Lake Argyle, Mitchell Plateau, Mount Barnett, Troughton Island, Warmun, Cockatoo Island, and Fitzroy Crossing.

The same system is set to bring heavy rainfall to the Northern Territory, with flash flooding possible in the Gregory and Tanami Districts.

A number of flood warnings have been issued in WA and the NT.

Australian Associated Press