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Yes, I think...in theory.
As long as you didn't do anything stupid like a single 120mm rad for two gpus then a 360 rad loop for the cpu.
It would keep the cpu and gpu from heating each others water. People mainly do it on rigs with lots of gpus and/or chipset and ram cooling. Keep in mind you would need two reservoirs and two pumps.
Got any plans on parts? Adding this to a current rig?
also, hdd watercooling seems a bit excessive to me but then again I suppose all watercooling is a bit excessive.
Edit: There is a section under "Overclocking & Cooling" dedicated to "Water Cooling" Might wanna check that out or get a mod to relocate this there.
http://www.xtremesystems.org/forums/showthread.php?254683-Dual-Loop-versus-Single-the-facts&highlight=dual+loop+vs+single
Worth the read even tho the pics are broken, the analysis and conclusion still gives you what you need.