NEW YORK—Can’t find an ATM from your bank nearby? Keep walking, or pay higher fees.

An annual survey from Bankrate. com found the average ATM fee for non-customers rose 12.6 percent this year to $2.22.

You’ll likely get dinged by your own bank, too. The average fee banks charge customers for using another bank’s ATM is $1.32, down from $1.46 in 2008, as some banks reduced or waived it.

About 72 percent of banks now charge customers a fee for using an ATM from a different bank, according to the survey. Nearly all banks charge non-customers for using their ATMs.

The average fee for overdrawing an account, meanwhile, rose 2.1 percent to $29.58 this year. In 1998, that fee was $21.57.

About a quarter of banks charge more for the second overdraft during a 12-month period. The average charge for the second to fourth overdrafts is $33.88. Bounce a third check, and a third of banks have an even higher penalty that averages $36.19.

“Even though the fees are moving higher, they’re completely avoidable,” said Greg McBride, a senior analyst with Bankrate.com.

That might be why banks are coming down harder on fees, he said—people are being more diligent about avoiding them. The American Bankers Association, an industry group, says most consumers do not pay any monthly fees for services.

The Bankrate.com study also found online accounts still provide better yields than traditional banks—0.69 versus 0.12, respectively. There are other benefits to online accounts, including lower fees and minimum balances.

The average minimum balance for online banks was $812.50, compared with $3,372.18 for traditional banks. If balances fall below the minimum, online accounts charged a $3.75 fee, compared with a $12.55 fee with traditional accounts.

Checking accounts that bear interest don’t seem to be a good deal. The average minimum balance is $3,372.18. The average fee for falling below the line is now $12.55, up 5 percent from last year. The trade-off? A measly average yield of 0.12 percent, down from 0.24 percent last year.

The data come from surveys with the five largest banks and five largest thrifts, and is based on deposits in the top 25 metropolitan markets in the country, according to BankRate.