From Dust Game Guide

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                            | The Roar of the Sea |                        [S3]
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This is the first mission where you have to deal with a real danger: cyclical
tsunamis. A timer appears in the upper right corner of the screen. When it 
hits zero, a big wall of water comes along and blows everything away. You'll
need the knowledge of Repel Water to keep your villages safe.

Capture the first totem and zoom out. Look around the waterfalls for a large
rock with a beam of light coming from it. This rock holds the knowledge of 
Repel Water. Start building bridges to connect your first totem to that rock, 
and once prompted, send a man over to the rock. The running water keeps trying
to wash the earth away, but if you pile enough on there, you can divert the 
flow. Once the man has reached the rock, he'll copy the knowledge onto a kite
and take it back to the village. The village is not safe until that man 
actually reaches it, so make sure he has a way back. You need to do all this
before the timer in the upper right corner reaches zero. Once that happens, the
tsunami hits. If your village is unprotected, it will drown. If it is 
protected, then the knowledge of repel water will allow them to keep danger at
bay. Note that repel water works for all water, not just the tsunamis. This 
village can never drown as long as it has the knowledge.

You won't be able to capture the second totem before the first tsunami hits,
so don't even bother sending anyone over. They'll just get caught in the wave
and die. What you can do is absorb the dirt connecting the repel water rock to
the main area. This lets the water that you had diverted previously flow back
in its original direction. You now need to build a bridge across the other 
streams to get over to the second totem. They are stronger and will require a
lot more earth, but it's definitely possible. The tsunami wave also doesn't 
reach this far up, so the earth will be safe from it. Alternatively, you can
have your men go around the long way and come up to the totem on the other 
side. This is a longer route, but the only bodies of water you have to cross 
aren't moving, so it's a little easier to make bridges. You'll also have to 
explore this large area anyway, since the portal is in here, probably covered
up by water after the first tsunami.

After capturing the second totem, make a bridge over to the portal area (if 
you haven't already). Move all of the water out of there and connect as much of
the dirt as possible. If you don't get the vegetation meter to 100% by the 
time the tsunami comes, the water will wash most of it away and you'll have to
work to get the meter back up. Also, it probably won't matter much here, but
it's worth mentioning that subsequent totems you capture don't automatically
come with any knowledge gained. Your second totem will not have the repel 
water ability until a guy from your first village comes over to the second one
with the knowledge. Make sure that you leave a route open for him. Once the 
portal is cleared, send your men to it and leave the mission once you've 
covered the area in vegetation. If it looks like you won't make it before the
tsunami hits, press B over the portal to cancel the order and your men will 
head back to the village. Just wait out the tsunami and then rebuild and 
continue on to the portal.