Cholera remains a problem in sub-Saharan Africa, especially in Malawi. Our aim was to investigate drinking water source quality compared with water treatment, risk perception and cholera knowledge for patients who had reported to a health center for treatment in the 2017–2018 outbreak in Karonga District, Malawi. The study analyzed 120 drinking water samples linked to 236 cholera patients. Nearly 82% of the samples met the national criteria for thermotolerant coliforms of 50 cfu/100 ml, while 50% met the more stringent World Health Organization criteria of 0 cfu/100 ml. In terms of the human dimensions, 68% of survey respondents reported that they treated their water, while knowledge of prevention, transmission and treatment of cholera was also generally high. However, of the 32 patients whose drinking water sources had thermotolerant coliforms of 200+ cfu/100 ml, 7 reported they felt a low or no personal risk for contracting cholera in the future and their community was extremely well prepared for another outbreak. The cost of a reactive response to cholera outbreaks puts a burden on Malawi, providing an opportunity for investment in innovative and localized preventive strategies to control and eliminate the risk of cholera while acknowledging social and cultural norms.