Staff had to place buckets on the floor of Bradford's multi-million pound refurbished Interchange to prevent it from flooding.
Customers attempting to buy tickets for bus journeys at the Travel Centre on the ground floor of the building had to dodge the dripping water as it poured down outside.
And station workers were kept busy mopping up a drip on the lower concourse, outside the WH Smith store.
The leaks follow a £2.7 million investment to develop a new concourse at the Interchange. Construction company Wates has been working on the project for more than a year.
A spokesman for Metro - the West Yorkshire Passenger Transport Executive - which owns the station, confirmed the building had developed two leaks but denied it was a design fault.
He said the leaks were caused by a blocked drain on the top bus deck while another part of it had become exposed while work was taking place.
"It's part of the process of renewing the waterproof membrane and we are exposing the deck in order to carry out this renewal," said the spokesman.
"It hasn't been helped by having one of the wettest springs on record.
"The bus station is being used all of the time so the work has to be carried out in phases.
"Our contractors are out working at the moment and our consultants are on hand overseeing the work being carried out. We are dealing with it."
Councillor Latif Darr, Labour spokesman for transport, said: "It's not good. If water is leaking on to the concourse, which is well used, then anybody could slip.
"The contractors and architects are 100 per cent sure that it is not a design fault. We hope it can soon be sorted out.
"We need to make sure this does not happen every time."
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