It should be "has" in your second example: "water" is the subject, and in the singular. The difference I see is that in (1) the water didn't actually flow to the sea, but in (2) it did. I'm sure others will add more comments...
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PhuongninhbaoI think we can substitue 'sea' by 'river'.Yes, though, of course, it depends on the context.
Phuong Ninh