The current terminals in Saint John and Digby were constructed in 1969 by the federal government under an agreement with Canadian Pacific (CP) and the provinces of New Brunswick and Nova Scotia.

On June 30, 2006, Bay Ferries announced plans to discontinue the Princess of Acadia service effective October 31, 2006 citing a 25% decrease in passenger totals since 1998.

The Nova Scotia government and Atlantic Canada Opportunities Agency offered a combined $6 million to subsidize the service, with additional funding expected from New Brunswick.

This ferry route was initiated in 1955 by the Government of Canada at the insistence of tourism operators and fish exporters in southwestern Nova Scotia.

Since the Gulf of Maine service operated to the United States, the vessel was not owned by the Government of Canada and was solely the responsibility of CN and later Marine Atlantic.

The city of Portland was in the process of constructing a replacement ferry terminal, but it assumed that financial difficulties would prevent Scotia Prince Cruises from returning to the Yarmouth service and entered into discussions with Bay Ferries about expanding its Gulf of Maine service to include Portland, in addition to Bar Harbor.

An announcement was made in late summer that Bay Ferries would include "The Cat" service to both ports from Yarmouth beginning in 2006 using HSC Incat 059.

Beginning with the 2006 and continuing into the 2007 operating seasons, the Government of Nova Scotia provided an annual $1.5 million subsidy to Bay Ferries due to declining passenger revenue and increased fuel expenditures.

The subsidy was increased by the provincial government for the 2008 operating season to $6.0 million to account for rising costs and further declines in revenue.

Bay Ferries had been seeking approximately $6.0 million for the 2010 operating season but the provincial government declined, citing financial difficulty.

In March 2016, only a few months after the closure of Nova Star Cruises, Bay Ferries Limited announced that it had reached an agreement with the U.S. Maritime Administration and the U.S. Navy for a multi-year charter of a new high-speed catamaran, HST-2.

[8][9][10] Service along this new route was originally expected to begin in summer 2019, but was delayed due to construction work at the Bar Harbor marina.

The HSC Incat 059 (still using its service trademark "The Cat") was taken from its seasonal layup to the Caribbean before returning to the Gulf of Maine for its regular six-month summer schedule.

The Government of Trinidad and Tobago has been in the process of trying to purchase a fast ferry to serve the inter-island route all year long.

On April 21, 2005 HSC Incat 059 became an indispensable link between the two islands after a Tobago Express aircraft had problems with its landing gear over the 'air bridge' route.