BackgroundDespite worldwide progress in terms of clean water supply, sanitation, and hygiene knowledge, some middle and most of low-income countries are still experiencing many diseases transmitted using unsafe water and the lack of sanitation.MethodsTo understand the impact of all waterborne diseases (WBD) registered in Ecuador. We performed a population-based analysis of all cases and deaths due to WBD in Ecuador based on the national public databases of hospital discharges as a proxy of incidence, in-hospital mortality, and countrywide general mortality rates from 2011 to 2020.ResultsIn Ecuador, mestizos (mixed European and Indigenous American ancestry) had the greatest morbidity rate (141/100,000), followed by indigenous (63/100,000) and self-determined white patients (21/100,000). However, in terms of mortality, indigenous population have the greatest risk and rates, having a 790% additional mortality rate (2.6/100,000) than the reference group (self-determined white populations) at 0.29/100,000. The burden of disease analysis demonstrated that indigenous had the highest burden of disease caused by WBD with 964 YLL per every 100,000 people while mestizos have 360 YYL per 100,000 and self-determined white Ecuadorians have 109 YYL per 100,000.ConclusionsIn Ecuador, waterborne diseases (WBD) are still a major public health problem. We found that indigenous population had higher probability of getting sick and die due to WBD than the rest of the ethnic groups in Ecuador. We also found that younger children and the elderly are more likely to be admitted to the hospital due to a WBD. These epidemiological trends are probably associated with the lower life expectancy found among Indigenous than among the rest of the ethnic groups, who die at least, 39 years earlier than the self-determined white populations, 28 years earlier than Afro-Ecuadorians and 12 years earlier than the mestizos.