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Can the bank/credit union charge me a fee when it transfers money from my savings account to cover an overdraft from my checking account?

Yes, if the fee was disclosed at the time you opened the account or at the time you authorized linking the savings account with the checking account, the bank or credit union can charge you a fee.

Usually, the costs of paying overdrafts from a linked account are considerably less than overdraft fees. You should compare the fees to other options to see what is best for you.