The amount of time it takes for overdraft protection to take effect depends partially on the type of overdraft coverage you have. Let’s say you have overdraft protection that allows you to go negative in your bank up to a certain amount without paying a fee. In that case, overdraft protection goes into effect immediately. But some overdraft protection programs automatically transfer the overdrawn amount from a linked savings or money market account. In that case, overdraft protection can take up to a few days to go into effect since that’s what’s required to transfer money from one account to another.