Mortality rates of some diseases are affected by water quality. This research examines the roles of two factors related to water quality, namely the quality of drinking water termed ‘water’ and the quality of sanitation termed ‘sanitation’. Two age-related diseases, cardiovascular disease and diabetes (CDD) and chronic respiratory conditions (CRC) are considered while adjusting for personal health issues, environmental and geographical factors. The dataset consists of worldwide mortality rates of adults for the mentioned diseases in 195 countries. These countries are clustered within continents geographically and literature shows the importance of considering the geographical effect of a continent. Furthermore, the two diseases were highly related to each other. Accordingly, the multivariate multilevel model was fitted to the dataset. The results indicated that when the usage of improved drinking water sources and sanitation facilities decreases, the chance of mortality from the two diseases increases. Furthermore, the difference in the risk of the diseases was statistically significant between the continents. It showed that North America and Europe had a lower risk of having CDD and CRC compared to Asia and Oceania. Therefore, the results revealed that the factors ‘water’ and ‘sanitation’ play important roles for this macro geographical variation of CDD and CRC.