Create Water doesn't create nearly enough water to flood deserts... but in hindsight, I really wish we'd upped it to be a 2nd level spell, because it IS a pretty disruptive spell to allow as a cantrip one can cast at will. And upping it to 2nd level gives folks two levels to play with "lost in the desert" adventures.
That said... if you have a character capable of casting the spell in your campaign, and if you haven't houseruled it up to a 2nd level spell or something, it's important NOT to "steal your players' toys." In the OP's situation, I'd go ahead and just stop tracking dehydration entirely and focus more on two other elements of survival—food and shelter. That's more or less the route I took for "Souls for Smuggler's Shiv," an adventure I wrote with PCs getting stranded on a deserted tropical island. Having to scrounge for food and shelter is, as far as feedback has indicated, more than enough to get across the survival themes without resorting to thirst as well.