Ipswich, Beenleigh, Logan City, Mud Island, the D’Aguilar Ranges and Cooyar would be affected by 5pm and Cleveland, Crows Nest, Helidon, Fernvale, southern waters of Moreton Bay and Peachester by 5.30pm.
Delaneys Creek recorded 62 millimetres in 30 minutes.
Brisbane Airport warned passengers could experience delays due to storm activity and urged them to check flight schedules with their airline.
Just before 3pm, ahead of peak hour, BoM issued a warning for damaging, locally destructive winds, heavy rainfall and large, possibly giant hail.
It warned that at 2.55pm, very dangerous thunderstorms were detected on the weather radar near Mulgowie, Grandchester, Rathdowney and Rosevale.
Very dangerous thunderstorms with giant hail, destructive wind gusts and intense rainfall were forecast to affect Laidley, Kooralbyn and Rosewood by 3.25pm and Ipswich, Beaudesert and Gatton by 3.55pm.
Other severe thunderstorms were detected on the weather radar near Lake Samsonvale, Dayboro, Kincora and Mount Nebo.
They were forecast to affect Pittsworth, Fernvale and Samford by 3.30pm and Strathpine, the area south of Toowoomba and south-west of Toowoomba by 4pm.
Damaging, heavy rainfall that might lead to flash flooding and large hail was likely.
Mulgowie received 62 millimetres in 30 minutes.
About 50 millimetres of rain was expected between Friday and Monday thanks to a combination of a low-pressure trough and onshore winds.
-with Jocelyn Garcia
Felicity Caldwell is state political reporter at the Brisbane Times