Water storage not working! I've got all my water available (Almost 1 Mil) and 0 in storage. All buildings..

It is very rare in the game to get water in reward chests (that go into your items inventory). The water value shown at the top is what is in storage in your water tanks (warehouse).

In general water is not needed for many things except sending to your Ration truck (there are a few buildings / research items that needed it though). Water is not used by troops and cannot be raided. In general, as long as your water Filters are built and upgraded a reasonable amount then you will not run out.