But many customers end up confused by how overdrafts work. In their marketing materials, for example, banks present the choice of whether to sign up for overdraft as an offer of “overdraft protection” — a feature many customers thought would automatically deny transactions and shield them from incurring the fees at all. In reality, it is a service authorizing the banks to charge the overdraft fees. Navy Federal Credit Union, for example, brands its product OOPS, or “Optional Overdraft Protection Service.”

“There was a push to frame ‘opt-in’ as a positive thing and sometimes gloss over the details,” said Samantha Kinney, who used to work at a retail bank and is now a financial counselor at Neighborhood Trust Financial Partners in New York.

Mr. Mangan, who works as a technology consultant, says he is the first to acknowledge that when he bounces a check, he should pay a penalty. But, one day last May, he noticed that TD Bank Group had charged him a $35 overdraft fee even though his account still had money in it.

That afternoon, Mr. Mangan withdrew $20 in cash at a TD Bank A.T.M., leaving only a few dollars in his account. That night, TD Bank processed a $125 check that he had written days earlier. As a result, the bank charged him two fees: one for the bounced check and another for the $20 A.T.M. withdrawal.

“I had that money in my account. I have the slip to prove it,” Mr. Mangan said.

The Consumer Financial Protection Bureau is hashing out rules that could limit reordering, according to people briefed on the matter but not authorized to speak publicly about it. Outlines of the rules are expected this year.

Still, the regulation is not a panacea, consumer advocates say. It will not address the lines of credit, which are considered loans. The credit lines are supposed to be less expensive than traditional overdrafts, and if customers pay off the loans quickly, the charges amount to only a few dollars.

But the costs can add up. KeyBank’s credit line, for example, carries a 15 percent interest rate, a $10 fee for every time customers overdraw their account, a $30 annual fee and $25 late fees.