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There is the Harbour Bridge Bus from Uptown to near the Ferry Terminal, it is about a 650m walk with the first 200m all downhill then flat. It should be about $15 if taking a taxi.

Saint John Marine terminal is on the East side of the Courtney Bay. From experience land crossing they do not care what you pick only that it has been completed. Even the barcode is only used at airports and they see it when they scan your passport