Human health is greatly affected by inadequate access to sufficient and safe drinking water, especially in low and middle-income countries. Drinking water governance improvements may be one way to better drinking water quality. Over the past decade, many projects and international organizations have been dedicated to water governance; however, water governance in the drinking water sector is understudied and how to improve water governance remains unclear. We analyze drinking water governance challenges in three countries-Brazil, Ecuador, and Malawi-as perceived by government, service providers, and civil society organizations. A mixed methods approach was used: a clustering model was used for country selection and qualitative semi-structured interviews were used with direct observation in data collection. The clustering model integrated political, economic, social and environmental variables that impact water sector performance, to group countries. Brazil, Ecuador and Malawi were selected with the model so as to enhance the generalizability of the results. This comparative case study is important because similar challenges are identified in the drinking water sectors of each country; while, the countries represent diverse socio-economic and political contexts, and the selection process provides generalizability to our results. We find that access to safe water could be improved if certain water governance challenges were addressed: coordination and data sharing between ministries that deal with drinking water services; monitoring and enforcement of water quality laws; and sufficient technical capacity to improve administrative and technical management of water services at the local level. From an analysis of our field research, we also developed a conceptual framework that identifies policy levers that could be used to influence governance of drinking water quality on national and sub-national levels, and the relationships between these levers.