Water security is essential for maintaining health and well-being, and for reducing a population’s vulnerability in a disaster. Among resource-poor villagers in China, water-related disasters and climate change may increasingly affect people’s water security. The purpose of this study was to explore the relationship between perceived water security and disaster risk perception in a rural ethnic minority community. A cross-sectional household survey was conducted in 2015 in Xingguang village, Chongqing, China, examining the association between villagers’ perceptions of household water security, disaster risk, and sociodemographic variables. Among 52 household representatives, 84.6% relied on rainwater as their main water source and 63.5% reported having insufficient water on a regular basis. Only 32.7% perceived themselves to be living in a high-risk area, of which climate-related disasters such as storms (44.4%) and droughts (38.9%) were the most frequently reported disasters in their area. Insufficient water quantity, previous disaster experience, and household members on chronic disease medication were found to be associated with higher disaster risk perception. Perceived water security indicators were not found to be predictors of preparedness attitudes and coping ability. Addressing water sufficiency in both disaster risk reduction strategies and long-term water management will be necessary to improve the health and livelihood of rural villagers in the coming decades.