A bonnie is a Scottish term that means "good, attractive, fine, pretty, and the like." Referencing "My Bonnie Lies Over the Ocean", Bonnie refers to a name of a person in this tune. This person in this folk song is Bonnie Prince Charlie (Charles Edward Stuart). He was born in Rome, Italy on December 31, 1720. He died in this same city on January 31, 1788.
The song is a story about Bonnie Prince Charlie in exile. He had led an uprising against the Georgian English in Edinburgh, Scotland; he was based in west Scotland. Subsequently, he attacked the English in England. He eventually retreated back to Scotland and then the Scottish Highlands as he faced opposition in Edinburgh. His forces were eventually defeated and he escaped the area and ended up on the high seas as he was taken out onto a ship destined for Skye.
"My Bonnie lies over the ocean
My Bonnie lies over the sea"
Bonnie is also the nickname of the St. Bonaventure sports teams (the Bonnies) at St. Bonaventure University in St. Bonaventure, New York. In the Atlantic 10, St. Bonaventure University has fourteen men's and women's intercollegiate teams in this competitive conference.
In addition, Bonnie is a popular female moniker as a first name. Bonnie is also a surname of families.
Generally speaking, "bonnie" is a Scottish word that means attractive or beautiful. It is often used to describe a woman and commonly used as a term of affection in a romantic relationship. Thus, this song may refer to the breakdown of a relationship.
In the context of this famous Scottish folk song, however, there is some speculation that "bonnie" refers to Charles Edward Stuart, a pretender (claimant) to the British throne. He was known popularly as Bonnie Prince Charlie.
In 1746, Prince Charlie's army was defeated at the Battle of Culloden, and he was forced to go into exile abroad. So, the reference to "bonnie" being "over the ocean" is, perhaps, a reference to his exile. In the next stanza of this song, Prince Charlie is urged to return:
Bring back, bring back
Oh, bring back my Bonnie to me, to me.
For more information on Bonnie Prince Charlie, see the reference link provided.
The word is also sometimes spelt as 'bonny'.