The number of free checking accounts continues to drop, following the sharp decline established in last year's Bankrate Checking Study. Just 45 percent of noninterest checking accounts are free of maintenance charges, down from 65 percent in 2010. That number peaked at 76 percent two years ago.

Overall, 60 percent more noninterest accounts carry fees and balance requirements than they did last year. And while economic factors may be a contributing factor, "the entire model of free checking has been turned upside down because of new regulations," Nagarkatte says.

In particular, he cites Regulation E, which forces banks to get a customer's opt-in before they can charge overdraft fees on debit transactions, and the Durbin Amendment, which limits the swipe fees banks can charge merchants for processing debit cards.

Tip: While free checking is in decline, more accounts have introduced waivers to avoid monthly fees, McBride says. Last year, 88 percent of noninterest accounts were either free or could become free if the customer signed up for direct deposit. This year, the number is 92 percent, which shows banks are still willing to offer checking for free in exchange for a deeper relationship with customers.

"Instead of getting the checking account for free, now you have to earn it," McBride says. "How do you earn it? On a noninterest account, it's direct deposit."