The lowest access to water and sanitation services in the city of Nouakchott leads to several practices and behaviours that create a social-ecological system which increasing risk of waterborne diseases transmission like diarrhoea. Using environmental, socio-economic and epidemiologic indicators from national statistic services, this study aims to assess the impact of Nouakchott’s social-ecological system on diarrhoeal diseases with particular emphasize on vulnerability to environmental health risks according to water and sanitation status. The results showed that respectively 25.6% and 69.8% of households had access to improved water sources and latrines with a large variability according to municipalities. The diarrhoeal morbidity (12.8%) was higher in dense urban areas where the lack of water supply and sanitation facilities affected mainly poor households (20.8% of the population). However, diarrhoeal risk is spatially variable in accordance to environmental sanitation disparities with a rate rising from 9.1% in municipalities with high level of improved water and latrines to 19.1% in communities with a lower level of ecosystem services. The correlation analysis between socio-economic, environmental and epidemiological variables reveals significant associations. Thus, the dynamic of social-ecological system demonstrated that environmental factors linked to unimproved drinking Water sources and sanitation services were the main driver of diarrhoeal diseases transmission in some municipalities. The reality of the linkage between health risks due to diarrhoea and urban environmental conditions addresses the issues of the Sustainable Development Goals (SDG) Health and Wellbeing and Water and Sanitation services in Mauritania context.