Purpose The evidence linking waterpipe smoking to cardiovascular disease is limited. We evaluated the association of waterpipe smoking (WPS) with arterial stiffness and wave reflection measured by augmentation pressure (AP), augmentation index (AIx), and carotid-femoral pulse wave velocity (CFPWV), which are validated predictors of cardiovascular disease. Materials and methods Community-based, cross-sectional study including 205 exclusive waterpipe smokers and 199 matched never-smokers aged 35 years or older (mean age 51.7 ± 8.9 years, 36% females). Smoking and its extent were assessed using a validated questionnaire and urine cotinine levels. CFPWV, AP, AIx (AP/aortic pulse pressure) and heart rate adjusted AIx (AIx@75) were determined using tonometry and compared between smokers and non-smokers, and the association of WPS with tonometry measures was assessed using linear regression adjusting for possible confounders. Results Waterpipe smokers and non-smokers had similar mean age and sex distribution. Compared to non-smokers, waterpipe smokers had significantly higher adjusted AP (10.5 ± 3.9 vs. 9.4 ± 3.9 mmHg respectively; p = 0.01), AIx (28.1 ± 8.4 vs. 25.7 ± 8.5% respectively; p = 0.01) and AIx@75 (24.2 ± 8.7 vs. 21.8 ± 8.9% respectively; p = 0.01). AIx was significantly associated with WPS extent, measured by a number of waterpipe smoked/day (β = 1.04/waterpipe, 95%CI:[0.50–1.58]), duration of waterpipe smoking (β = 0.77/10-years, 95%CI:[0.16–1.38]), their products in waterpipe-years (β = 0.30/10-waterpipe-year, 95%CI:[0.12–0.47]) and plasma cotinine (β = 0.56/100 ng/ml, 95%CI:[0.14–0.98]), adjusting for possible confounders, and so were AP and AIx@75. CFPWV however, was not associated with waterpipe smoking. Conclusion In a community-based sample, exclusive WPS and its extent were associated with a dose-dependent increase in AIx and AP, accounting for other risk factors, suggesting that waterpipe smokers are at increased risk of cardiovascular disease.