Wells Fargo, for instance, could lose between $568 million to $1.1 billion in revenue, according to a recent report by financial advisory firm Sandler O'Neill & Partners.
JPMorgan Chase, the country's second-largest bank, is roughly in the same neighborhood, with projected losses ranging from $544 million to just under $1.1 billion.
Bank of America would be the biggest loser, according to the report, with its revenues expected to take a hit of between $1.1 billion and $2.2 billion.
Among the big four banks, Citigroup, the country's No. 3 bank by assets, is poised to see the smallest losses as a result of the new Fed rules -- between $65.8 million and $131.6 million, according to the report. The bank does not currently charge overdraft penalties but does allow consumers to link their checking accounts to other accounts, for a fee, to cushion against overdrafts. Other banks offer similar services.
Sandler O'Neill managing director Kevin Fitzsimmons said that while new, higher checking account fees may be in the works, banks are also trying another strategy to stem these losses -- aggressive marketing designed to convince consumers to, as the new Fed rules allow, "opt in" to overdraft plans that will continue charging them overdraft penalties.
"They'll definitely try and get as many customers to opt in as they can," Fitzsimmons said.
But banks can't rely on just getting any consumers to sign up for overdraft protection, Bankrate's McBride said. Only a small percentage of consumers -- between 14 percent to 17 percent, according to different studies -- account for most overdraft fees paid. It's in the banks' interest, he said, for those consumers in particular to opt in to overdraft plans.
How successful banks will be remains to be seen. Fitzimmons notes that customers may ignore marketing materials promoting overdraft protections. Banks, he said, may have more success convincing consumers to sign up for overdraft protection later this summer after those who are low on funds actually start to see their debit cards rejected by retailers.
Some customers, however, say they'd rather get their cards rejected than be hit with overdraft fees.
Joanna Pecina said she learned her lesson after racking up nearly $120 in overdraft penalties. Pecina, of Houston, said in a message to ABCNews.com that she would not opt in to an overdraft plan.
"Though the idea of being rejected at Macy's hurts my ego, at least I won't be feeding the bank's pocket any more than I have to," she said.