The jar at the bottom of the hookah is filled with water sufficient to submerge a few centimeters of the body tube, which is sealed tightly to it. Deeper water will only increase the inhalation force needed to use it. Tobacco or tobacco-free molasses are placed inside the bowl at the top of the hookah. Often the bowl is covered with perforated tin foil or a metal screen and coal placed on top. The foil or screen separates the coal and the tobacco, with the foil and the tobacco reaching maximum temperatures of 450 and 130 degrees Celsius respectively. These temperatures are too low to sustain combustion and considerably lower than the 900 degrees Celsius found in cigarettes.

A larger fraction of the smoke condensates of the hookah are produced by simple distillation rather than by pyrolysis and combustion and as a result, would tend to carry considerably less of the pyrosynthesized compounds found in cigarette smoke. As a result of suction through the hose, a vacuum is created in the headspace of the water bowl sufficient to overcome the small static head of the water above the inlet pipe, causing the smoke to bubble into the bowl. At the same time, air is drawn over and heated by the coals. It then passes through the tobacco mixture where due to hot air convection and thermal conduction from the coal, the mainstream aerosol is produced.

The vapor is passed down through the body tube that extends into the water in the jar. It bubbles up through the water, losing heat, and fills the top part of the jar, to which the hose is attached. When a user inhales from the hose, smoke passes into the lungs, and the change in pressure in the jar pulls more air through the charcoal, continuing the process. Vapour that has collected in the bowl above the waterline may be exhausted through a purge valve, if present. This one-way valve is opened by the positive pressure created from gently blowing into the hose.