A surcharge was an additional charge added on top of usual fees to account for unusual circumstances.
In 2372, a four percent surcharge was added to a shipment of Karemman fleece to pay for an inspection to determine if Changeling infiltrators were hiding in it. Hanok complained to Benjamin Sisko about the taxes and fees being levied on the Karemma by the Federation, citing this as an example. Quark defended the charge, saying, "You never know where they might be hiding." (DS9: "Starship Down")