The impact of climate change has made weather events more extreme, unpredictable and frequent. In the last 4 years, Mozambique has been devastated by 8 major cyclones, resulting in material and human damage and affecting the functioning of basic local services, such as in the water and health sectors. In this study, we explored the environmental components of the climate–water quality–disease relationship that could drive the dynamics of waterborne diseases. Statistical models and geospatial information technologies (GITs) were used to analyse water quality and the relationship with waterborne diseases between 2016 and 2023. Results indicate that water quality is the main element, between precipitation natural disasters and waterborne diseases, on which a relevant public health intervention can act to ameliorate the future negative impacts of climate change and disease incidence. The results of this study also showed that the quality of water affected mainly by heavy rain events varies in different regions and in different seasons. Keywords: climate change; flood; water quality; waterborne diseases; integrated water resources management