Background: Access to safe, affordable and accessible drinking water is a human right and foundational to the third and sixth World Health Organization’s Sustainable Development Goals (SDGs). Unsafe drinking water is a risk factor for chronic and enteric diseases. Both chronic kidney disease (CKD) and diarrheal disease are highly prevalent in the Lake Chapala basin, Jalisco, Mexico, suggesting disparities in factors leading to successful achievement of these two SDGs. Methods: This study aimed to assess progress towards SDG three and six in the Lake Chapala basin. Qualitative, quantitative, and geospatial data were collected between May and August of 2019 from three towns within the municipalities of Poncitlán and Chapala. Results: Ninety-nine households participated in this study. Water sampling analyses determined 81.18% of samples from water jugs (garrafones) and 70.05% of samples from tap water were contaminated with total coliform bacteria, often including E. coli. Additionally, 32% of garrafón samples and 61.9% of tap water samples had detectable levels of arsenic. Approximately 97.94% of respondents stated that they believe clean water is a human right, but 78.57% feel the Mexican government does not do enough to make this a reality. Conclusions: This mixed methods approach highlights water quality as a serious issue in communities around Lake Chapala, and demonstrates inadequate drinking water as a key hazard, potentially perpetuating the high disease burden of both CKD and enteric disease in the region.