Watching someone cry sets off a chain of thoughts in the speaker, and each one comes back to water. Too much of anything, even something natural, can hurt. Waves are a good example: like people, they can bring joy and pain both. The speaker seems to be gently saying that the person's sadness is part of a bigger pattern, not something strange or shameful.
The ocean gets special attention. Even on its "bad days," when it is rough, it joins with the cliffs to make the one sound that keeps the speaker sane. That suggests that painful or stormy things can still offer comfort. The final lines tie it together: tears and waterfalls are the same water, and only the cause of the fall differs. The mood is tender and calm. Rather than rushing to fix the crying, the speaker offers quiet understanding, comparing it to something large, natural, and even beautiful.