[2] The airline initially operated seaplane sightseeing tours with De Havilland Canada DHC-6 Twin Otters, prior to obtaining its FAR Part 135 status and beginning scheduled passenger service in 1994.

[2] In late 2008, the airline launched land-based air services to San Juan from both St. Thomas and St. Croix, under the "Seaborne Airshuttle" brand name.

[4] On December 15, 2010, the airline announced new services to San Juan's Luis Muñoz Marín International Airport from St. Croix, St. Thomas, and Vieques, for launch on January 12, 2011.

[13][14][15] On October 23, 2013, Seaborne Airlines announced its first destination in the Dominican Republic, with service to La Romana International Airport beginning on December 12, 2013.

[16] On November 7, 2013, the airline announced new routes to Saint Kitts and Nevis, with service to both Robert L. Bradshaw and Vance W. Amory International Airports starting on January 15, 2014.

[17] On December 18, 2013, Seaborne Airlines announced it was relocating its headquarters from Christiansted, St. Croix to San Juan, the move of which was completed by March 2014.

[26] On March 5, 2015, Seaborne announced Air Europa as its fifth airline partner, with the two airlines codesharing on Seaborne's flights from San Juan and Air Europa's flights from Adolfo Suárez Madrid–Barajas Airport to Santo Domingo's Las Américas International Airport, effective from March 29, 2015,[27] although the codeshare agreement ended at a later date.

The airline announced the acquirement of a $4.2 Million credit facility and entered a purchase agreement with Silver Airways, which was subject to the Court's approval and potential overbids.

[43] The list does not include destinations served only by its parent company Silver Airways, with which the two airlines share operations based at Luis Muñoz Marín International Airport.

[7] Each aircraft had a different marine animal painted on the tailfin, consisting of a dolphin, lobster, manta ray, marlin, octopus, seahorse, sea turtle, or shark.