Will my customer see the extra charges a hotel collects at check in, like city tax or a resort fee, before they pay on my website?

Yes, in most cases your customer will see those charges before they pay, but it depends on what the supplier sends through for that hotel.

Hotel rates arrive from your suppliers as a room price plus, separately, a note of anything the property collects directly at check in. That can be a city or tourist tax, a resort or facility fee, or a charge for parking or cleaning. When the supplier sends that information in a form the portal can read, it is shown under the room price on the search and booking pages, worded as payable at the hotel rather than added to the amount your customer pays you. It is also carried onto the confirmation voucher, so the guest has it in writing when they arrive.

Where this gets less tidy is that suppliers are not consistent with each other. Some send these charges as plain text buried in the room description instead of as proper data, and in that case the portal can only display the text as it came through. Local taxes also change from time to time, and some are worked out per person per night, so what is quoted at the time of booking is the supplier's best statement rather than a promise from the hotel. If you connect more than one supplier, you may well find the same hotel describing its extras differently on each connection.

The useful thing to do next is to run a few test searches on the cities you sell most often and read what actually appears under the price for those hotels. If a supplier you rely on is sending nothing at all, raise it with them, and in the meantime you can add your own standing wording to the voucher so your customers are never caught out at the desk.