Background: Tobacco prevention research traditionally focuses upon cigarette smoking, but there is also a need to implement and evaluate the usefulness of waterpipe tobacco smoking (WTS) interventions since it is considered less harmful than cigarettes. This study aimed to assess the impact of an educational intervention on WTS knowledge of health professional students in three academic health institutions in Bahrain. Methods: A quasi-experimental design was used to include medical students from the Arabian Gulf University, medical and nursing students from the Royal College of Surgeons in Ireland-Bahrain and nursing students from the University of Bahrain. Two hundred fifty students participated in the three phases of the study during October 2015-June 2016 from an original sample of 335. The participants answered knowledge questions on WTS before and after an intervention, which included a lecture by an expert and a video on the awareness about the health hazards of WTS. Results: The mean age of starting cigarette and WTS was 16.8 ± 2.8 and 17.5 ± 1.7 years, respectively. The prevalence of ever smoking any type of tobacco among students was 22.4% (medical 25.8% and nursing 37.5%) and that of WTS, 17.7% (medical 20.0%, nursing 13.6%). The prevalence of current cigarette smoking was 9.6% among medical and nursing students combined with 10.3 and 8.5% for medical and nursing students, respectively. WTS was prevalent at a proportion of 6.8% among medical and nursing students combined with 6.5% in medical and 14.8% in nursing students. The university curriculum as the main source of knowledge on WTS increased from 14.2 to 33.3% after the intervention (p < 0.005). Knowledge about the hazards of WTS increased in 16 of the 20 statements. The difference in overall knowledge score was significant (p < 0.05) for nursing (77. 5 ± 1.5 vs 85.8 ± 2.2) compared to medical students (85.3 ± 1.0 vs 87.3 ± 0.9) after the intervention. Conclusions: Our educational intervention with health professional students improved their knowledge about the health effects of WTS. Medical and nursing institutions may consider using various methods such as informative videos and expert lectures to include in their teaching curricula as part of WTS prevention strategies. © 2018 The Author(s).