Cancun has no single harbour. Ferries leave from a terminal north of downtown and from two hotel-zone beaches; the tour boats leave from marinas on the lagoon behind the hotel strip. Turning up at the wrong water is the most common way to miss a sailing here.
Puerto Juarez — signposted as Gran Puerto — is the real ferry terminal, at Av. López Portillo SM-84 north of downtown, the address Ultramar publishes on its own routes page. The crossing from here is the shortest anyone runs: 15 to 20 minutes, roughly every half hour. It is also where the whale-shark boats and most Isla Contoy trips load, being the closest quay to the open sea north of the island.
Playa Tortugas sits at Boulevard Kukulcán km 6.5 and Playa Caracol at km 9.5, both inside the hotel zone. Same Ultramar fare, longer crossing — 25 to 35 minutes, because the boat has to clear the bay first — and a thinner, roughly hourly timetable. Ultramar's fare page adds a line worth reading twice: at Playa Caracol the dock fee is not included.
Marina Aquatours, also at km 6.5 but on the lagoon side, is where the Isla Mujeres catamarans load; its own site lists a boarding fee of 15 USD per person, adult and child alike, cash at check-in. The jungle-tour docks further along the lagoon charge more — operators publish a 20 USD per-person marine-use fee, cash on the day, described as a federal charge for use of the marine natural elements. Neither appears in the booking price.
Punta Sam, further north again, is the car ferry and nothing else: UltraCarga runs it four times a day on weekdays, at 06:00, 10:00, 14:00 and 18:00, the crossing takes about 45 minutes, and you must arrive an hour early to buy the ticket. Golf carts rent on Isla Mujeres itself, so unless you are moving a vehicle it has nothing for you. The R-1 bus links every other waterfront — hotel zone to downtown to Puerto Juarez, around the clock, 12 pesos in cash to the driver — which is why a Puerto Juarez departure is no obstacle even from km 20.