The word "عين" in Arabic is a classic example of a polysemous word (مشترك لفظي) - a single word with multiple meanings determined by context. Its meanings include:
ينبوع - a spring or source of water
عضو في الجسم - the eye (body organ)
جاسوس - a spy
ذات الشيء - the thing itself (essence)
In the sentence "عين الماء صافية" (the water spring is clear), the word عين is paired with الماء (water) and described as صافية (clear/pure). This context makes it clear that عين here refers to a ينبوع (spring/water source) - the natural point where water emerges from the ground.
It does not refer to the eye (body organ), as eyes are not described as "water springs." It does not mean a spy, as that meaning has no connection to water. And while عين can refer to a place in some expressions, the specific collocation with الماء points definitively to a water spring.