Waterpipe tobacco smoking has become increasingly popular in recent years, especially among youth. We aimed to understand longitudinal trends in the prevalence and user perception of waterpipes and their flavors on Twitter. We extracted waterpipe-related tweets from March 2021 to May 2022 using the Twitter Streaming API and classified them into promotional tweets and non-promotional tweets. We examined the longitudinal trends regarding the waterpipe flavors mentioned on Twitter and conducted sentiment analysis on each waterpipe flavor-related non-promotional tweet. Among over 1.3 million waterpipe-related tweets, 1,158,884 tweets were classified as non-promotional and 235,132 were classified as promotional. The most frequently mentioned waterpipe flavor groups were fruit (34%), sweets (17%), and beverages (15%) among all flavor-containing non-promotional tweets (17,746 tweets). The least mentioned flavor groups were tobacco (unflavored, 4%) and spices (2%). Sentiment analysis showed that among non-promotional waterpipe-related tweets, 39% were neutral, 36% were positive, and 23% were negative. The most preferred waterpipe flavors were fruit, mixed, and alcohol flavors. The least preferred flavor groups were tobacco and spice flavors. Our study provided valuable information on the prevalence of waterpipe flavors that can be used to support the future regulation of flavored waterpipe tobacco products given the nature of the current regulations on other flavored tobacco products.