Fetching details from the dictionary...

to become clear (water, air, etc.); to become transparent
to resonate clearly (e.g. voice)
to become serene; to become tranquil; to be free of worries
to pronounce as an unvoiced sound
秋になると空気が澄んでくる。
The air becomes clear in autumn.
この湖の水は本当に澄んでいる。
The water in this lake is really clear.
彼女の目は澄んでいて美しい。
Her eyes are clear and beautiful.