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On two occasions earlier this month, floods shut down several subway lines, leaving many New Yorkers wondering how a few inches of rain could bring the system to a grinding halt. WNYC's Beth Fertig has more on where the water goes.

When Joe Joyce goes down into the subway, he's not looking into the tunnel. He's looking at the drains lining the tracks, each with the potential for turning a subway station into a wading pool. And the drains need lots of maintenance.

JOYCE: It doesn't take much debris to clog that up. One newspaper or plastic bag and then the water can't get in.

Joyce is the Transit Authority's Superintendent for Hydraulics, making him the man in charge of drains and pumps. We're walking along the tracks at a subway station in Brooklyn where Joyce is pointing to the drain-boxes.

JOYCE: That was one of the earlier attempts...

The newest models have rectangular lids that can be fifteen feet long. They're much bigger than the old ones which were small and easy to clog. The drains aren't just there for a rainy day.

JOYCE: Even without rain we pump 13 million gallons of water a day, without rain.

That's because many of the subway tunnels were dug below the water table. They're waterproofed but after 100 years they're showing their age. Water enters the system in all kinds of ways - leaky ceilings, vents, staircases and leaky water mains. And most of it is ably diverted.

There are 289 pump rooms to collect the water. This one in Brooklyn happens to be the largest one.

JOYCE: There's 650 gallons a minute coming into the room here.

We're standing at the edge of a hatch, where the water is surging fifteen feet below in a sump. If it starts to rise because of natural buildup or a storm, four submersible pumps automatically kick into action.

These alternating pumps divert the water to storm sewers so it won't spill out onto the tracks. Joyce turns them on to demonstrate and the water level drops significantly.

But even the largest pumps, working at a thousand gallons a minute, are no match for serious downpours like the ones that swamped the subway tracks earlier this month. It's not that the pumps aren't working, says Joyce.

JOYCE: I'll give you the best analogy I can give you. You turn on the water in your sink in the morning, right. If you turn it on slow the water goes down the drain no problem. But if you turn it on full force the water will kind of build up in the sink a little bit before it drains off. I mean it's still going down but you can see some water building up in the sink. Cause you've reaching a point of capacity of the pipe.

And that's what happened in the subway system this month. Water rained down at a faster rate than the pumps and sewers could handle it, collectively. But at the height of hurricane season, it's hard to imagine how the city could be caught off guard.

FERTIG: Why can't you warn passengers or let the city know, today there's a likelihood subway system can get flooded.' JOYCE: September 8th, the forecast - I receive 3 weather forecasts a day. September 8th the forecast didn't tell me it was going to rain so we didn't even put any preventive measures in place because we didn't know we were going to get that kind of storm.

Even so, he says, there's still a limit to how much the sewer system can take. This week, Joe Joyce and his hydraulics department did plan for the worst. Teams were sent out before yesterday's rain. The Transit Authority acknowledges it can still do more to prevent track flooding. The MTA's proposed capital plan would spend 126 million dollars to upgrade the drains and refurbish the oldest pumps so they can handle more water. Some date back to the 1930s. But transit officials say even those are still working fine. For WNYC I'm Beth Fertig.