Erdem, We probably need more ...

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Erdem, We probably need more detail on your problem, but if I understand correctly you want to take a network of streams and ascribe each segment to one of your 3 classes? Perhaps you could use a flow accumulation approach using a DEM? Calculate the flow accumulation along your stream network - and then compare the flow accumulation values with streams that you know are perennial or intermittent. If you have a reasonable sample of streams with known characteristics this can work - although you may need to account for variability in rainfall and/or geology if you are doing it over a wide area.