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The upheaval in today’s economy is forcing banks to find new ways to strengthen their bottom lines—and much of that effort is coming at your expense.

Increasing service charges and widely varying interest rates are just two of the techniques banks are using to pump up their slumping profits during these troubled economic times. According to the Kiplinger Letter, overdraft and credit card fees will climb 5 percent in 2009, double the 2008 increase. Late fees for credit payments will soar and ATM fees may jump 20 percent.

This situation could cost you real money unless you learn how to play by the new rules of the game.

Here’s how:

1. Keep an eye peeled for sneaky bank charges

In a largely invisible ploy, some banks make customers pay big penalties for small errors.

Let’s say you accidentally overdraw your checking account. You have $300 in the account and you write three checks in one day. The first is for $10, the second for $20 and the third for $320. Some banks process checks not in the order they receive them, but in order of size. In such a case, the bank will process the $320 check first. That would mean all three checks, not just one, would bounce. Then you’d be hit with three separate overdrawn check charges. Since those have risen to $35 at some banks, you could be out as much as $105 in painful overdraft charges.

Crystal Watkins, a vice president at Torrey Pines Bank in San Diego, suggests signing up for an overdraft protection line of credit, available at most banks. “This would be much less expensive than the heavy fees incurred when a check bounces,” she says. “When money is tight, as it is now, you don’t want to lose any of it to unnecessary fees.”

2. Ask for a waiver

These days, the banking industry is more competitive than ever, and as a result many banks are willing to waive such charges as late fees, overdraft fees and check printing charges—but only if the customer asks. If the service rep can’t help you, ask to speak with a manager.

Certified financial planner Christine Moriarty of Bristol, Vt., suggests going to the branch that opened your account to ask for a waiver, since that branch will have the most flexibility. “But don’t ask too often,” she cautions. “They’re not going to do it on a regular basis.”

3. Invest wisely in certificates of deposit

Certificates of deposit have long been considered a safe haven for conservative savers with cash to invest. CDs insured by the Federal Deposit Insurance Corp. are still among the safest ways to protect your principal, but the new economy has brought about important changes that affect CD investors.

The Federal Reserve’s steady lowering of short-term interest rates has affected long-term CDs to the point where the return on a five-year CD may not exceed the inflation rate. That’s why you should stay away from long-term CDs until interest rates rise.

Jeff Harris, a registered investment adviser and author of Retire Rich and Happy (Aames-Abbott Publishing, 2006), points out that you can buy CDs through your broker instead of banks. “That’s especially advantageous for customers who have large sums they want to cover with FDIC insurance without having to drive around from bank to bank,” he says. “Brokered CDs allow customers access to banks all over the country competing for deposits. This way, customers can not only enjoy very competitive interest rates, but have all their FDIC-insured CDs show up on a monthly statement.”

4. Avoid allowing maturing CDs to roll over automatically

When you receive a notice that your CD is maturing, call or visit the bank and ask to review all current interest rates, including any promotional rates that may be available. An automatic renewal will often get you something less than the bank’s best available rate.

“A maturing CD presents a good opportunity to come in and visit in person with your banker,” says Watkins. “That’s a good chance to develop or renew a personal relationship with your local manager while you review all of the current CD rates.”

5. Always shop around for the best interest rate

Bank deregulation has produced a highly competitive environment with widely differing interest rates. If you can find a better deal than your present bank is offering, take it. A new website called MoneyAisle makes it easy to compare CD rates from scores of banks in an automated auction.

Using the site’s simple interface, enter your state, the amount of your deposit and the CD’s term, and then sit back and look over the offerings. Pick the best deal or walk away—there’s no obligation. All participating banks are FDIC-insured. “While it’s not perfect,” says Jim Bruene, editor of Online Banking Report, “it’s a simple research tool that can help you get a better deal on your CD purchases.”

6. Say goodbye to that financial behemoth

Is your bank larger than the gross national product of some countries? If so, does it treat you as a valuable asset? Does it exercise economies of scale in order to bring you superior services?

Not likely. Experience has shown that many of the megabanks resulting from merger mania are raising inefficiency and customer alienation to new heights.

Fortunately, solving this frustrating problem is relatively painless. Just search out the smallest FDIC member bank in your neighborhood and give it your business. It’ll be happy to have you as a customer, and you’ll receive more personal attention from a community bank than you ever will at a financial behemoth. Even the smallest bank, as long as it’s an FDIC member, will give you the same insurance protection as the largest bank.

“For the most part, the small community banks did not get involved in the subprime business, strange investment products and high-risk ventures,” says Moriarty. “They tend to be run better as a business.”

Even at a small bank, you should follow the principles outlined in this article, but you’ll be doing it in a friendlier atmosphere. Fewer banking frustrations will let you enjoy your stroll down the path to financial security.

7. Skip the bank, look into credit unions

According to some credit union fans, the best way to beat the banks is not to use them. “When I hear my friends complaining about bank fees and service charges, I tell them to look into credit unions,” says Maureen Sherman of West Nyack, N.Y. “I don’t worry about what new fees my credit union is tacking on to my account because, as a member-owned, not-for-profit organization, I know they have my best interest at heart.”

For the most part, credit unions offer the same products and services that you’ll find at your local bank. Most offer an array of checking, savings, mortgage and consumer loans, online banking, bill pay, investment and insurance products—often with no or lower fees than other financial institutions.

Because credit unions are owned by their members and not outside stockholders, members stand to benefit from a more service-oriented approach. Unlike banks, credit unions return all earnings to their members in the form of higher dividend rates on savings and investment accounts, lower interest rates on loans and reduced or no-fee products and services. 

William J. Lynott is an author and freelance writer who specializes in business and financial issues.