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Ohne Wasser werden die Pflanzen aussterben.

Ohne Wasser werden die Pflanzen vergehen.

Are aussterben and vergehen interchangeable?

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Your first sentence doesn't make sense. aussterben means to die out in the sense a whole species dies out, like for instance

Der Orang Utan ist vom Aussterben bedroht.
Der tasmanische Tiger ist ausgestorben.

In your second sentence vergehen could be used in that context, but I would rather use the word absterben, which means to die off

Ohne Wasser werden die Pflanzen absterben.

vergehen is usually used with events and time like

Die Zeit verging wie im Fluge.
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    Well, the first sentence is also right, if you want to say that when there's no more water on the earth, plants will die out. – PMF Jan 4 '14 at 9:33
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    @PMF You could say that, but then Ohne Wasser werden alle Pflanzen absterben. would be more correct idiomatically in that context. – Stefan Haberl Jan 4 '14 at 9:41
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    Hmm... I'd rather say that as Ohne Wasser wird alles Leben auf der Erde aussterben. Talking about the worlds end. – PMF Jan 4 '14 at 10:08
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    Definitely. No the work's done, let's have a drink at the bar at restaurant at the end of the universe. ;) – Stefan Haberl Jan 4 '14 at 10:22
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    Oh, I heard they served good waiter's legs... – PMF Jan 4 '14 at 10:32
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Aussterben is simply to die out. You wouldn't use it for one single plant in your room in English and it works the same in German.

Vergehen means to pass (the intransitive version) and it can go in many directions one of which is to whither away. You can use it for pain or love and if you want you can also use it for plants (not for animals and humans). That would be a rather high brow use though. The common term for the basil plant on the window sill is eingehen.

So botton line... the two words have no overlap and they are never interchangeable.

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You could use "eingehen" for animals or plants in the sense of dying.

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