Background: While cigarette smoking has been considered the most relevant tobacco product worldwide, waterpipe tobacco smoking (WTS) has increased in prevalence globally and calls for more considerable attention now. However, little is known about WTS cessation knowledge and clinical practices among physicians, particularly in Lebanon. This study aims to examine the knowledge, barriers, and cessation practices of primary care practitioners towards WTS. Methods: A cross-sectional study where an anonymous self-reported questionnaire was completed by physicians attending the Annual Conference of the Lebanese Society of Family Medicine for family medicine physicians, general practitioners, and internists in Lebanon. Results: Out of 180 attendees, 105 primary care practitioners (PCPs) responded to the questionnaire. Only 38.1% of the physicians think similar techniques are used for the cessation of smoking of both cigarette and waterpipe. Similarly, 30.5% of the physicians believe that nicotine replacement therapy works in the cessation of waterpipe smoking. There was a statistically significant difference between the percentage of physicians who counsel for cigarette smoking and those who counsel for waterpipe smoking cessation (p = 0.005) where 30% of the physicians tend to counsel against cigarette smoking more than waterpipe smoking. Conclusions: This study shows a difference in the attitude and behavior of PCPs towards cigarette and waterpipe smoking cessation. Moreover, there is a lack of knowledge about water pipe smoking cessation techniques. There is a great room for continued medical education to PCPs in their private practice to improve their knowledge.