Typically, yes. Although it depends on the bank. With most banks (at least the larger ones), you will get a notification that your account is going to overdraft if you do not deposit funds. That will buy you enough time to get more money into the account right away.
Banks settle their accounts at the end of each banking day. If the account is overdrawn at the end of the banking business day you will be assessed an overdraft fee. If you make a deposit prior to the end of the banking day and you have a positive balance at this time you will typically not incur an overdraft fee.
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