Access to clean water is important for menstrual hygiene practices, an important aspect of health for adolescent girls. In Bangladesh, adolescent girls represent poor menstrual hygiene practices, whereas the practice is worse among vulnerable population groups living in areas experiencing seasonal water scarcity. This study portrays perceived difficulties in menstrual hygiene practices among indigenous adolescent girls during the period of seasonal water scarcity in Bandarban Hill District, Bangladesh. Data was collected from 242 indigenous adolescent girls through interviews during the period of water scarcity. Backward stepwise regression model was used to identify factors associated with perceived difficulty in maintaining menstrual hygiene (PD) practices. The study participants, mainly living in hard-to-reach areas, reported difficulty in getting adequate water during the water scarcity period, and the quality of water was reported to be poor. PD due to water scarcity was found to be significantly associated with water source degradation (β = 0.247, < 0.001), the need for boiling/purifying water before use for menstrual hygiene (β = 0.203, p = 0.005), and experience of water availability when it was necessary to maintain their optimal menstrual hygiene practice (β = 0.449, p < 0.001), time required to collect water (β = 0.209, p < 0.001), taking a bath every day (β = -0.228, p < 0.001), and frequency of washing genitals per day (β = - 0.094, p = 0.040). Indigenous adolescents perceive difficulty in menstrual hygiene practices during the period of water scarcity. Further research could be carried out to observe to what extent the seasonal water scarcity could be attributable to worsen the menstrual hygiene practices and to identify the need for addressing the problems.