I think the problem is logical rather than grammatical. Absent eddy currents, the water is flowing at any and every given point in a stream. "The point where the water is flowing" refers to any point where the water is not stagnant.
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AvangiUsually relative adverbs, such as where and when, are used instead of 'which + preposition.This is the house in which I lived/which I lived in.
This observation leaves me scratching my head. Sorry.