Wellington City Council will be looking at what's going on underneath Adelaide Road, following flooding on its surface yesterday morning.

For the second time in two years a carpark near the Basin Reserve was flooded - and an emergency medical centre above had to be closed.

Council spokesman Richard Maclean says council will look at the storm water system following the floods, but says there will always be areas the system can't cope when the rain is that heavy.

"I guess the unfortunate position we're in is we have to decide whether to spend millions upon millions expanding the capacity of the stormwater system."

He says a big decision looms for the council.

"Those are the issues that we're going to have to look at and see whether we have to get in there and decide whether there are easy things that can be done to fix the situation or whether it has to be a bigger fix."