Background The use of the Asian tobacco waterpipe (TWP) in the Lao People's Democratic Republic represents a potential communal source of infectious disease. This practice of smoking can lead to weakened defences of a smoker's respiratory epithelium, making the smoker vulnerable to respiratory diseases such as coronavirus disease 2019, tuberculosis and others. Methods This study evaluated the water quality and hygiene factors among 43 smokers of five villages in rural Luang Namtha Province. Water samples were collected from participant's TWPs and assessed for the presence of Escherichia coli, coliforms and aerobic plate count (APC) bacteria using the 3M Petrifilm. Results The microbial indicator testing results were 95% positive for the APC, 38% positive for coliforms and 17% positive for the E. coli indicator. The concentrations were highest for the APC, with an average of 106 colony forming units (cfu)/ml, followed by coliforms with <100 cfu/ml and lowest for E. coli with <10 cfu/ml. Most TWPs were infrequently cleaned, heavily used and contained a warm, brown-coloured water. Conclusions The warm, dark and moist internal water container may facilitate microbial survival and growth. The use of a TWP adds several unstudied modes of transmission to a complex and common biobehavioural and environmental pathogen exposure. Future TWP cessation activities should be tailored to consider risks of infectious disease transmission.