These two expressions, “d’œufs” and “d’eau”, are actually pronounced differently :

• “d’œufs” is pronounced like “deux” (the number 2)
• “d’eau” is pronounced like “dos” (the back)

But indeed, there are several situation where different words are pronounced in the exact same way (for the record, they are called homophones). In these cases, you need to rely on the context to identify the correct meaning. Situations where different homophones can make both interpretations of the sentence meaningful are quite rare.

If think one of the worst example of this is the group “ver / vert / vers / verre” which are all pronounced exactly the same :

• “un ver” : a worm
• “vert” : the color green
• “vers” : can mean both “towards” (“Je vais vers la maison.”) or be a verse in poetry.
• “un verre” / “du verre” : glass, the object or the material

But in most cases, only one can make the sentence meaningful :

• “L’arbre est vert.” : “The tree is green.”
• “Je vais vers la maison.” : “I’m going towards the house.”
• “J’ai un verre d’eau.” : “I have a glass of water.”
• etc…

There’s also context, in addition to the above answer, or if you cannot tell them apart for some reason. Same with homophones in English.