The flooding that crippled the city’s subway system yesterday created a drought, of sorts, for businesses that scrambled to open on time and saw fewer of their regular customers coming through their doors.

New Yorkers who were turned away at their subway stations or got stuck trying to get onto a packed bus arrived at work hours late, throwing appointment books into disarray and leaving many businesses with a shortage of employees for much of the morning. The economic damage resulting from lost productivity and reduced foot traffic has not yet been assessed. But some merchants are already claiming losses and at least one business leader is warning that a rain-triggered collapse of the subway system does not aid New York as it is tries to maintain its edge as the world’s leading global marketplace.

The CEO of The Partnership for New York City, Kathy Wylde, said the half-day of chaos would, at the very least, mean short-term losses.

“If you think about 3 million people going to work and the fact that a substantial portion of them lost half their day, that’s going to be a lot of money,” Ms. Wylde said.

She said the fact that a “15-minute storm could knock out the city’s entire transportation system” could also shake confidence in the city as a place to do business. She said that while the short-term losses were not likely to be severe for large businesses, those companies need to believe in the solidity of basic services. If they don’t, they won’t continue to locate jobs and expand operations here.

The chief economist at the Reis Inc., Sam Chandan, said the impact of a transit meltdown is far less substantial now than it would have been 10 or 15 years ago, because it has become so easy to work from home.

The city’s Economic Development Corporation said yesterday that the 2005 transit strike cost New York between $440 million and $660 million a day. And, while yesterday’s breakdown may not have been as severe, it was reminiscent, with commuters walking over the Brooklyn Bridge and trudging through commutes that lasted hours.

The Bloomberg administration started going block-by-block to meet with businesses in areas affected by the storm. The commissioner of the city’s Small Business Services, Robert Walsh, said his agency would match small businesses with financial grants. It was unclear how much money that businesses would be eligible for or if that money will be available for those who lost money solely because of transit delays, rather than direct storm damage. Stories about disrupted workdays abound. Dr. Mike & Son, a barbershop on Church St. in TriBeCa, estimated at least a 30% loss of customers yesterday. The owner, Mike Babaev, said he couldn’t open until after noon.

The manager of Blue Spoon Coffee on Chambers Street, Drake Aldrich, said the coffee shop did 75% less business than usual. “It was dead this morning,” he said. A lawyer at the American Arbitration Association, Sandra Partridge said she turned around after making “only three blocks worth of progress” in more than an hour. “I’m going home to telecommute for a few hours and to hose down,” she said as the heat index soared.

A Flatbush resident, Susan Roberts, who was in Lower Manhattan yesterday morning trying to get to 63rd Street and Third Avenue where she works as a nanny, didn’t have the luxury of turning around. Her employer, she said, was waiting for her to arrive before leaving for work herself.