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If we have referral particle in the middle of the river, will it's velocity increase with higher river level?

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If I understand you correctly, then yes. This page, for example, has an image showing a typical velocity profile. The water moves slower near the bottom because of friction.

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Yes, You understand it well, but I think that this friction -> velocity dependency is not do big... in real world, when river level is about 2m higher... – danmaslo Feb 1 '13 at 9:45
That may well be true. The name for the part of the flow that's slowed down is the "boundary layer", and in a large river it might be quite a bit smaller than the height of the water. But it will also depend on a lot of things, including the speed of the flow, the roughness of the bottom, and the shape of the river channel. here is some information about boundary layers in rivers. (I haven't read it, so I don't know if it's useful.) – Nathaniel Feb 1 '13 at 11:22

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