Background Despite evidence for the harms of waterpipe tobacco smoking (WTS), its use is increasing amongst college and university students worldwide. This systematic review aims to assess the knowledge of, attitudes towards and perceptions of WTS among college or university students. Methods We electronically searched MEDLINE, EMBASE, CINAHL, PSYCHINFO and ISI the Web of Science in October 2018, restricting our search to studies published since January 1990. We included studies among university or college students that used qualitative or quantitative methods, and addressed either knowledge, attitudes, or perceptions towards WTS. We excluded studies where WTS could not be distinguished from other forms of tobacco use and studies reported as abstracts where the full text could not be identified. Data were synthesised qualitatively and analysed data by region (global north/ south), and by reasons for use, knowledge of health hazards, how knowledge influences use, perceptions towards dependence, and policy knowledge. Results Eighty-six studies were included; 45 from the global north and 41 from the global south. Socio-cultural and peer influences were major contributing factors that encouraged students to initiate WTS. Furthermore, WTS dependence had two components: psychological and social. This was compounded by the general perception that WTS is a less harmful, less addictive and more sociable alternative to cigarette smoking. Knowledge of WTS harms failed to correlate with a reduced risk of WTS use, and some students reported symptoms of WTS addiction. A large proportion of students believed that quitting WTS was easy, yet few were able to do so successfully. Finally, students believed current public health campaigns to educate on WTS harms were inadequate and, particularly in the global north, were not required. Conclusion Reasons for WTS amongst university students are multi-faceted. Overall, interventions at both the individual and community level, but also policy measures to portray a message of increased harm amongst students, are required. Additional studies are necessitated to understand temporal changes in students’ beliefs, thus allowing for better targeted interventions. Electronic supplementary material The online version of this article (10.1186/s12889-019-6680-x) contains supplementary material, which is available to authorized users.