"This will mean some changes to service times and timetables, increased travel times, and delays when the harbour is busy before, during and after racing," said the alert.
Ferry passengers were also warned everything could change at a moment's notice on race days, saying if possible people might want to consider rescheduling travel outside race day periods.
Affected ferries included the Waiheke Island service which would operate under a 45-minute frequency from 2pm on race days, and take 70 minutes until speed restrictions lifted at 7pm, and the Devonport service which would run every 20 minutes and take 15-20 minutes to cross the harbour until 8pm.
Gulf Harbour ferries would be replaced by buses on race days.
There were no timetable changes for Coromandel, Rotoroa Island or Bayswater ferries.
There would also be additional services for Hobsonville, Half Moon Bay and Birkenhead.
As well as altered timetables ferry passengers were warned to allow extra time for navigating foot traffic in downtown Auckland.
"With over 200,000 visitors expected in the Auckland CBD over the America's Cup period, Auckland Transport are advising all Aucklanders and visitors to plan their journeys in advance, expect longer travel times and allow extra time for navigating foot traffic in downtown Auckland," said the alert.
"If possible you may want to consider re-scheduling your travel outside of race day periods, as journey times will be longer and may be subject to delays on the day as well."
Fullers360 chief executive Mike Horne said the ferry company had worked closely with Auckland Transport and the harbourmaster to deliver an appropriate race day timetable that reflected the required limits and restrictions in place for vessels travelling in the harbour on race days, while prioritising customers' needs.
"Fullers360 has been planning for the busy America's Cup racing schedule with the relevant transport and maritime authorities to ensure we provide consistent and reliable services to Aucklanders and visitors.
"We have designed a bespoke race day schedule to accommodate the longer sailing times that are a result of the lower speed restrictions advised by the Harbourmaster.
"We recognise that these race day timetable changes will have a flow-on effect on local communities.
"We believe our race day timetable will minimise the inevitable disruptions of a busy America's Cup racing schedule on the water."