If you've ever completed a merchant account application, you should have noticed the category, "NSF fee" or some variation of the term.  The agent should have explained that the credit card processor will charge you a fee in the event that there are rejects -- amounts that were unable to be collected by the processor.  Typically, the industry average NSF fee is $25 although this does not include the sum that your bank may also assess.

Now NSF bank fees may not impede cash flow too much as the cost is rather modest but you're not considering the domino effect of insufficient funds.  Indeed, merchant account providers will typically hold your future batches until they collect the money they are rightfully owed.  Here, you're expecting automatic deposits (from credit card transactions) into your account and the spigot stops flowing.

Many times, you won't even realize that your funds have been cut off until several days, perhaps even a week or longer, as many merchant account providers will not promptly tell you about this situation (i.e., that they were unable to collect a fee and are holding funds).

Consider Joe Q. Merchant who is paying $30 for a wireless monthly fee.  The processor tries to withdraw that sum but the ACH is unsuccessful.  Now Joe is on vacation and does not realize that his bank account is in the red.  A couple of days later, the processor tries to collect the $30 again with the same negative result.  Joe will be charged the $25 NSF bank fee twice ($50) and his own bank will add to Joe's woes by assessing their own insufficient fund fee two times as well.

This collection process will happen a third time, and unfortunately, the processor once again can't take blood from a stone.  Hence, Joe will be hit with a third NSF bank fee (from both the processor and his bank).  Now, the merchant account provider may not only expect the original $30 and the $75 (arising from the three individual NSF fees), but may have placed an additional hold of say, $300, due to risk issues. 

Joe comes back from vacation and finally learns about the matter, discovering that he will not be paid until his batches go over $400!  Now his cash flow is seriously impeded. 

The moral of the story: Joe Q. Merchant, meaning you, cannot afford to let the merchant account / bank account go low in funds.  You always should maintain a healthy balance in your account (at least a couple of hundred dollars) to avoid the above scenario.  This is particularly important as more processors are charging annual PCI compliance fees that may reach above $100 in cost.  Such a cost will automatically be deducted from your account.

Study, learn, and know your bank balance to avoid the dreaded insufficient funds tag.  (Perhaps the words, "overdraft protection" must become part of your lexicon.)  The credit card processing funds spigot always needs to be on ... and the NSF bank fee spigot always needs to be off.