I could perceive the ship coming over the horizon.

I know "horizon" means a line between the earth and the sky but I cannot understand the above sentence with this meaning.

So could you explain to me what "over the horizon" means here?
Your first paragraph is fine, Anon. The second isn't. If it is over te horizon, you can't see it at all.
Hi, User_Gary.
I could perceive the ship coming on the horizon.
Over in that context means that the ship is on the plane surface of the water far away from us an it appeared.
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Thank you.Fandorin.

So you mean horizon means "the plane surface of the water" here. Am I correct?
Horizon means the line between sky and water.
And "the ship coming over the horizon" means the ship appeared far away on the horizon.
Indeed, horizon in that meaning can be explained in this concrete situation like you wrote above.
Horizon is the apparent line that divides the earth and the sky (Collins Dictionary).
The ship is coming towards you but is not yet visible, it is beyond or on the other side of the horizon. As it moves over the horizon you perceive it, first as the top part of smoke/sails/masts/funnel come into view and then it is all visible. It has come over the horizon and is in your field of view.

So it means that you know something is coming to you but you do not know the details of what it is yet as it is "over the horizon".
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 fivejedjon's reply was promoted to an answer.

What's the meaning of over the horizon?