There were up to 30-minute delays starting around 5 a.m. because the train control system was not working properly through the tube. Trains had to run in manual mode and reduce their speed, BART spokeswoman Alicia Trost said.
The control room where the computer system is kept had water seeping through the ventilation system and computer equipment got wet, Trost said.
After drying out the equipment, the computer was rebooted and trains could resume running automatically around 8 a.m., Trost said.
However, weather-related delays continue to slow down travel times.
Trost said many trains have been switched to manual mode as rain pelts tracks and makes for slick conditions. There are 15-minute systemwide delays, she said.