It's probably being provisioned to other settlements. Or they're drinking it.
Put a container next to your workbench (or whatever other workbenches you have) and empty the water into it.
Do you have a caravan between that settlement and another, if so the caravans will transport water to the other settlements if their water is low.
Also as rylasasin has wrote move stuff out of the workbench if you want to keep it as the workbench contents are treated as resource.
This ^^^
If you leave the water be for too long the settlers will use it. For all I know they're taking long showers or something, but they will use it. Empty the bench out every time you return to base and it should solve your problem.
empty everything from the "aid" category, then next time you show up it will have water