The last decade has seen an increasing trend in consumer preference of bottled water over tap water. Little is known what type of water children and adolescents prefer for drinking and what their parents think of their community tap water. The study objective was to assess drinking water preferences, perceptions of the qualities of tap water and bottled water, and fluoride knowledge in an urban pediatric population. We conducted an anonymous survey of a convenience sample of caretakers of children and adolescents at an urban clinic regarding their preferences for tap or bottled water, their perceptions of the quality of tap and bottled water and their knowledge of fluoride. Of the 208 participants (79% African American, 9% Latino), 59% drank tap water, 80% bottled water. Only 17% drank tap water exclusively, 38% drank bottled water exclusively, 42% drank both. We found no significant differences in water preferences across age groups, from infancy to adulthood, or among ethnic groups. Ratings for taste, clarity, purity and safety were significantly higher for bottled water than tap water (P < 0.001). Only 24% were aware of fluoride in drinking water. We conclude bottled water was preferred over tap water in an urban minority pediatric population. Perceptions of the qualities of water seemed to drive drinking preferences. Public health strategies are needed to increase public awareness of the impact of bottled water consumption on oral health, household budgets and the environment.