I get charged everytime a deposit is made into my account. Are those charges coming from Quickbooks?

If these deposits are being processed through Quickbooks Payments then yes, that is the service fee for processing the deposit. https://quickbooks.intuit.com/payments/pricing/ goes over how much Intuit charges for the deposits. If you are using a different third party to process payments then that may be charging a service fee. It's important to pick this fee up as an expense so that your sales are accurately recorded. For example, if 10$ is withheld from the deposit then a journal entry should be made that credits sales for the amount and debits Service Charges or an equivalent expense account. Hope this helps!