Is this on your E36 318is? You should only have 2 bolts holding your water pump in:
There are four holes, because two of the holes are used to remove the water pump. The extra two holes are simply tapped bores so that you can insert an M6 bolt in each, tighten each bolt a little bit a a time (try to keep them even), and force the water pump off. Use the bolts that hold the thermostat housing in place.
From the diagram from realoem, it seems to me that the holes on the top left and bottom right are the ones for the bolts that hold the pump in place. The other two are the tapped bores for the M6 bolts.