Best way to filter water out of oil when pumping in oceans?

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First: Build a well around your oil, so that the pump doesn't try to pump the ocean dry.
After that, if you still have some water in there, simply add a small tank, prefilled with one bucket of water, to the line. If that tank isn't enough, your pump seems to still tap into the ocean, so patch that hole.
 
interesting. i'm using fuel now and the larger oil wells i've pumped have all been on land. i suppose getting respiration on a helm or making air pockets below the surface and using scaffolds to "frame" the oil away from the water would work. I haven't used scaffolds but i believe that you can just click the original block to make a vertical structure. it would make blocking the water off easier i believe ;P
 
Scaffolds should probably work (hadn't thought of that ... nice :)). You can also encase the column of oil with a gravity-affected block like sand or gravel.
 
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Gregtech Advanced pump.
Had to say it.
Although you will need to update GT if you have it, its fairly new in the Release.
 
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I just build a casing around the well from sea floor to surface; takes care of most of the problems. The gregtech advanced pump might be nice, if I could find more than "hey this got added" information on it. *sigh*
 
Do the TE portable tanks or BC glass tanks only accept one type of liquid once they are started?

If so, using 2 tanks let some water and some oil accumulate in each.

When the water one is full use a gate to pump out a little and void it.

When the oil one is full pump it onto its next destination.

This should ensure your 'filter' tanks always have the right fluid in them.