yes, gpus are very good coolable by water. it depends on your videocard, but in most cases the gpu-fan is the loudest fan of the system - if there is no fan on the northbridge.

But you can cool them both by water and enjoy the silence...
But as i said above, if you replace your gpu-cooler with a watercooler you should ensure that there is some slight aircooling for the capacitors and mosfets of the card - or select one of the special vga-coolers who cover the whole card. but these are mostly suitable only for one card, and if you buy a new card, you also need a new cooler.