Water resources in the Chia lagoon in Malawi experience a possible threat to sustainability. Communities are seeking alternatives to improve water quality in the lagoon. This study quantified the communities’ willingness-to-pay (WTP) and their influencing factors while using contingent valuation (CV) techniques. A wide range of data collection procedures, including focus group discussions, key informant interviews, field observation, and CV survey, were employed. A sample of 300 households was randomly selected. The CV results showed that 57.4% of the households were willing to pay. The monthly individual aggregate WTP amount ranged from MK696.83 (US$0.95) to MK81697 (US$111.38), and on average MK7870.45 (US$10.73), generating aggregate annual values ranging from MK6, 689,568 (US$9126.29) to MK784, 294,080 (US$1,069,978), and on average MK75,556,320 (US$103,078) (ceteris paribus). Logistic regression model demonstrated a significant (p < 0.01 or p < 0.05) relationship between demographic (gender, age, literacy level), social-economic (land ownership, main agriculture water source, and income), and institutional (civic education and social network, extension, institutional trust, household socio trust) factors and WTP. The findings from this study provide significant clues for further research and baseline information for local government and communities in the development of more effective and holistic approaches for improving water quality in natural ecosystems.