The highest rainfall in the region was recorded in Karratha, where 209.2mm of rain has fallen since 9am yesterday.
The rainfall smashed Karratha's daily June record of 60mm.
Roebourne Airport recorded 135.8mm, Karratha Airport recorded 209mm, Port Hedland 129mm, Barrow Island 73mm and Paraburdoo 52.4mm.
Main Roads reports that the North West Coastal Highway is closed to all traffic between Roebourne and Port Hedland.
The Weather Bureau has issued flood warnings for Pilbara coastal rivers.
Further heavy rainfall of 50mm to 100mm with isolated heavier falls is expected in the the Turner and Yule River catchments and inthe Port Hedland area during today.
Karratha worker Martin Tscheuschler said there had been heavy rain overnight.
He said water in the mining site in which he worked was "a foot deep, maybe two in some places".
Minor flooding is expected to continue in the Maitland River and extend toother streams between Karratha and Port Hedland during today.
The State Emergency Service advises people and communities to be aware that flooding is possible and be prepared to relocate equipment and livestock.
WATCH: Pilbara Floods.
Travellers need to be aware that road conditions may be adversely affected and travel plans may need to be reconsidered.
Do not drive into water of unknown depth and velocity.
Weather Bureau duty forecaster Rabi Rivett said the rainfall was caused by a small tropical low and a trough out to the north-west of the Pilbara, which interacted with a front and caused a cloud band and heavy rainfall.
"This is very unseasonable rainfall," he said. "The highest totals have been right on the coast.
"It's normally the type of rainfall you would see with a cyclone."
The Department of Education says Baler Primary School, Nullagine Primary School, Marble Bar Primary School, Hedland Senior High School, Roebourne District High School and Wickham Primary School have all been affected by flooding.
Roebourne/Wickham Road is closed but the Department says the water is starting to recede.
Work is being carried out on a roof leakage at Baler Primary School. There is also no power or a landline phone connection at the school.
Most students at Hedland Senior High School from outlying areas have been unable to attend school due to the flood waters and bus services from Point Samson, Wickham and Roebourne to Karratha Senior High School have been cancelled.
Emergency services warned residents in coastal catchments between Onslow and east of Karratha and those in the Ashburton and Fortescue River catchments to prepare for possible minor flooding overnight and today.
The rain is expected to weaken as it moves away from Karratha and starts streaming over Port Hedland throughout the morning.
Heavy falls are expected through the eastern and inland areas of the Pilbara, with the rain moving over the Kimberley by Thursday.
In the south of State overnight, North Island received 16mm of rain, Bunbury recorded 15.2mm, Collie East 10.8mm and Witchcliffe 10mm. Dwellingup recorded 17.8mm while Perth received 7.8mm of rain.
Isolated showers are forecast for Perth today, with a maximum of 19C.
The showers are expected to continue in the south tomorrow before conditions become sunny or partly cloudy by the weekend. - Yahoo.