It is normal for approximately 2.5 to 5 cm of water to remain in the upper chamber. Because the BOROUX Legacy™ water filter is a gravity-fed water filter, it relies on the pressure and weight of the water to push it downward and through the filters. As the water flows into the lower chamber, there is less and less weight pushing it downward (water pressure in the upper chamber decreases). Additionally, the water cannot flow through the plastic Stem Saver.
You can discard any remaining water if you're refilling the top reservoir of your BOROUX Legacy™ water filter.