Customers at Primark were evacuated on Commercial Road following the torrential rain at around 3pm.
Shoppers waited outside in the hope of the store re-opening before the shutters were later closed by staff.
They claimed they had been asked to leave by staff because the floors had become too slippery.
Marlene Knight, who was visiting Bournemouth for the day from Reading, said she had been left disappointed by the shop’s closure.
“Ironically I wanted to get into Primark to get something to keep me dry,” she added.
“I am hoping it opens again soon.”