It means to be confused or not understand something at all.
A state of complete disorder.
I was at sea when he started discussing quantum physics during dinner.
When the teacher asked him a question about the subject, he was at sea.
Even the judge was at sea listening to the unreasonable requests from the plaintiff and his lawyers.
A medical professional sometimes gets a case that would put him at sea, at such time he would himself recommend a second opinion.
There is no origin for this idiom
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definition
Common phrase that has a specific meaning.