[Straight Vermonter]

The scientists raise a few other possibilities – one is that Qumran’s residents waterproofed this particular jar by lining it with gypsum. It then could have been used to store water or another type of liquid. “Against this hypothesis is the fact that there have been no previous reports of gypsum lining of such jars,” the team writes.

I'm no expert but I'm pretty sure gypsum is water soluble so it wouldn't make a very good waterproofing substance.

[spokeshave]

Maybe they used it to store gypsum

[SunkenCiv]

The gypsum definitely works, but not indefinitely, it’s what the Nabataeans used to line their cisterns. And, it had the great virtue of being readily available. :’)