Yes it is normal and not unusual for the last 1.3 cm. to 2.5 cm. of water to remain in the upper chamber. By design the water must pass through very fine micro pores within the elements in order to pass from the upper chamber to the lower. The lower the water level in the upper chamber, the lower the pressure available to force the water through the micro pores. You may have noticed that the system filters much faster when full than when half full. That’s because there is more water pressure. The only way to remedy this problem would be to enlarge the pores of the filter elements. This would of course, reduce the efficiency of the Berkey system. During each cycle the water left from the previous cycle mixes with the water from the current cycle and is then filtered. There is no need to be concerned about the excess water during normal use. Should you however discontinue using your filter for a period of time such as during a vacation, it would be best to empty both chambers before departing and leave them upside down to dry on the dish rack.