I smoked two hookah pens...I inhaled it...It had water vapor coming out and it was flavored. Will it show up in a drug test? I'm peeing in a cup.

Drug test. This depends on what was in your hookah pen. If it had fruit flavorings only, it will likely not show up on a drug test. However, if it had thc, nicotine, or others in it, these could show up on your drug screen if testing for those. You need to know also that these vapors can be irritating and damaging to lungs. http://www.fda.gov/forconsumers/consumerupdates/ucm173401.htm.
They do not. They do not test for tobacco or shisha in a drug test.