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Sobre vs. encima de vs. por encima de

The Spanish words sobre, encima de, and por encima de all describe physical positioning related to being over, above, or on top of something. While they can sometimes be used interchangeably, their main differences depend on whether the objects are making physical contact, their exact vertical alignment, and whether movement or open space is involved.

Sobre

The word sobre is the most general and versatile term used to indicate that something is on, on top of, or over another object. It most frequently implies direct physical contact like an object resting on a surface, but it can also be used for things hovering or passing directly over something.
Dejaste tus llaves sobre la mesa del comedor.
(You left your keys on the dining room table.)
El avión vuela sobre la ciudad.
(The airplane flies over the city.)
Puso una manta gruesa sobre la cama.
(He put a thick blanket on top of the bed.)
Caminamos con cuidado sobre el hielo.
(We walked carefully over the ice.)
Derramó un poco de café sobre la alfombra.
(She spilled some coffee on the rug.)

Encima de

The phrase encima de translates to on top of, heavily emphasizing an exact vertical alignment or stacking. It is a more specific alternative to sobre when you want to highlight that one object is physically resting directly upon another, often as a distinct layer.
El gato siempre duerme encima de la silla.
(The cat always sleeps on top of the chair.)
Guarda los zapatos encima del armario.
(Keep the shoes on top of the closet.)
Llevaba una chaqueta de lana encima de la camisa.
(She wore a wool jacket on top of her shirt.)
No te sientes encima de mis gafas.
(Do not sit on top of my glasses.)
Puso el pastel de chocolate encima del mostrador.
(He placed the chocolate cake on top of the counter.)

Por encima de

The phrase por encima de means over or above, specifically highlighting a lack of physical contact or a trajectory passing higher than an object. It is the best choice when describing clearance, elevation, or movement across an airspace without touching the surface below.
El pájaro voló rápidamente por encima de los árboles.
(The bird flew quickly above the trees.)
Lanzó la pelota por encima de la valla del jardín.
(She threw the ball over the garden fence.)
El nivel del agua le llegaba por encima de las rodillas.
(The water level reached above his knees.)
El helicóptero pasó por encima del edificio principal.
(The helicopter passed over the main building.)
Mantén tus manos por encima de la mesa durante el juego.
(Keep your hands above the table during the game.)

Summary

In summary, use sobre as your everyday, general word for on or over. Choose encima de when you specifically want to emphasize that something is physically resting directly on top of something else. Finally, opt for por encima de to highlight that there is a clear physical gap between the objects or that something is passing high above a surface.