Neither yet, nor already indicate surprise. Usually when you use the word "yet" it means that there is an understanding that it will happen. For example: Have you bought new shoes yet? The asker knows that they are going to buy new shoes but they are uncertain if they have or have not. If somebody says, " I haven't done that yet. " it means hat they are planning to but have not. I Already can mean the same but it indicates that something has been done before. They both fit in the context in which you wrote but the two words are not always interchangeable.

En realidad, tienes razón: Las dos frases pueden servir para ¿regaste las plantas ya? (como preguntando si se ha hecho algo que se esperaba que se hiciera para ese punto), pero solamente el uso de "already" implicaría que no se esperaba que lo hubiera terminado ya. Otros ejemplos de esto son: You are 16 and you have finished highschool already? ¿Sólo tienes 16 y ya has temrinado la secundaria? He is already there? ¿Ya está allí? Espero que esto te ayude.

I end the "yet" with a rising tone that I don't use with "already". I tend to end with al RED y to indicate astonishment. I lower the tone for disgust at wasting my time if they were not yet watered.