The BOM warned that the storms could produce heavy rainfall that would lead to flash flooding in Sydney and other areas in NSW.
The storms disrupted public transport and flights on Monday afternoon.
The storm warning was issued for Sydney Harbor Bridge, the Olympic Park, and the waters off Bondi Beach until 4 pm.
The storms then moved northeast and were expected to affect areas such as St Leonards, Manly, Dee Why, and Chatswood by around 3:30 pm.
The NSW State Emergency Service responded to 49 calls for help due to the storm outbreak. One of these involved a car stuck in Eastgardens.
A spokesperson for the SES said that most of the calls they received were about damaged or fallen trees and roofs in areas such as Macarthur, the City, and the Inner West.
Minor flood rescues were also reported. Sydney Airport reported that a couple of flights had been delayed due to the storm.
A spokesperson for Sydney Airport said that due to the storm activity, some flights had been delayed. People should check with their airlines for the status of their flights.
Light rail services were also disrupted, with the L3 Kingsford and L2 Randwick lines not running due to the flooding at Kensington.
The NSW State Emergency Service warned that the storms and heavy rainfall that were expected to affect the east coast over the next couple of hours could cause flash flooding in Sydney and other areas.
People should avoid driving through flood water and stay away from storm drains and creeks.
If they become trapped in flood water, the SES said they should seek shelter in the highest area and call 000.