You are missing the GregTech way of extracting Water from a River.
GT6 replaces Water Blocks in Rivers with Riverwater Blocks, which are infinite. Now I do not exactly know why Buildcraft Pumps dont even recognize my Water, but I do know that it works fine for GT6 ways of draining Water.
If you want an Infinite Water Source to power your Boilers and such, use a Drain Cover placed on a Pipe to drain infinite Water from a Riverwater Block.
If you want to get rid of the Water inside the River because you absolutely hate Rivers, use the Rotational Pump, which will drain the Riverwater until nothing is left.