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Banking with your mobile? There will be a fee for that...

As more and more customers are using their mobile devices to make deposits or pay bills, the banks are looking for ways to charge them for the service.

While fees for using mobile apps may be inevitable, the banks differ only over how to levy that charge.

Some banks believe it should be a fixed cost per transaction, others believe fees should only come on products that present risks to the bank and provide unique services to the customer, such as Regions Financial for immediate funds, and Wells Fargo for emergency bill pay.

Still others — who asked not to be identified because the strategy hasn't been announced — have lobbied for a model resembling "Amazon Prime," where customers pay a flat fee for unlimited transactions.

Birmingham, Ala.-based Regions Financial rolled out its mobile banking app this spring with a tiered fee structure, based on when the customer needed access to funds deposited digitally. For immediate availability, which is a risk to the bank because it then doesn't have time to verify the fees, customers must pay $5, or a percentage of the deposit—whichever is higher. For access two days later, once the funds are verified, the fee is 50 cents—the same fee Minneapolis-based US Bank introduced for all mobile deposits in 2010. It was the first bank to initiate such fees.

"This is just the beginning of the creative ways banks will try to compensate in a low-rate, low-growth environment," said Todd Hagerman, senior research analyst at Sterne Agee. "They have to look for alternative ways to improve their fee income stream."

Customers like Al Falussy, a sales executive on Long Island, NY, are not happy. He is a frequent user of his mobile banking app to get balance alerts, send money to employees and family, and deposit money from places where no branches are nearby.

But if Falussy's bank of choice—JP Morgan Chase—started charging to use the app? He'd switch banks.

"They're making money on my money," Falussy said of the deposits he keeps with the bank. "So for them to actually go there would be kind of petty."

Falussy and other consumers might not like it, but fees for mobile banking are set to become the norm. Slowly but surely, banks are experimenting with ways to build charges into the apps' features and as apps get higher-tech, too, a simple convenience could become costly.

(Read More: Banks Still Raising Fees—and Hiding Them: Study)

Richard Hunt, president of the Consumer Bankers Association, said banks can't afford to give customers all services free of charge, especially because of increased regulatory and legislative pressure. For one example, "checking accounts were often provided at no cost to the customer, but there is a cost to the bank providing them." Innovation on mobile, Hunt said, will fall into that category.

(Read More: Overdraft Protection Will Cost You, But How Much?)

Dave Kaminsky, a senior analyst at Mercator Advisory Group, a research firm focused on the payments industry, explained that users perceive mobile banking's offerings as worth the cost. "Customers tend to look at remote deposit capture or expedited processing as an additional value, so they're willing to pay for it—at least for now."

Customers seem to be embracing mobile banking fees so far. US Bank, a source said, hasn't experienced many customer defections since the fee was introduced in 2010. And even though Regions has the steepest fees yet, CEO Grayson Hall said on the company's last earnings call that mobile "continues to be a rapid growth channel." Perhaps one reason is that mobile, as a platform, is still surging in growth: The number of web-savvy consumers who bank only on their app jumped 55 percent in the last year, according to digital measurement outfit comScore.

Still, customer sensitivity to fees looms large as many big banks are hesitant to be the "first mover" in the space—and potentially lose customers to their competitors. JPMorgan Chase currently offers all its mobile features for free and will continue to do so, according to a person familiar with the matter.

"Deposits will eventually move from ATMs entirely to mobile," said an executive familiar with the strategy. "You want to capture that business, not turn it away." No direct fees are levied for ATM deposits.

Wells Fargo has been the only major bank to experiment with fees thus far. The bank refuses to charge for remote check deposit, which totaled 1.4 million checks in May alone, because it considers the service basic. Instead, it has chosen to charge for what it considers to be premium mobile services, like bank-to-bank transfers and emergency bill pay.

Features like emergency bill pay and immediate availability of funds are risky for banks, since it takes time to verify that the funds exist on the end of the check writer. Because banks must pay for insurance in case the money isn't there, a fee to have the money available immediately would simply cover that insurance. For that reason, at least three big banks have lobbied regulators like the Office of the Comptroller of the Currency, according to people familiar with the talks, to discuss options to verify funds without having to charge customers.

At a time when consumers feel buried in fees by their banks, one more charge tacked on to services could prompt more consumers to follow Falussy's game plan to hang up on their bank.