Gold mining activity is a source of supply in many areas of the world, and especially in developing countries, it is practiced illegally and by applying unsafe techniques. Particularly in Ecuador, artisanal and small-scale gold mining (ASGM) is widespread, and it is based on the use of toxic substances, such as mercury (Hg), in gold recovery. Hg is a heavy metal that is water-insoluble, which, once mobilized, poses a threat to both the environment and human health. This study analyzes Hg concentrations in the six provinces of Napo, Sucumbíos, Orellana, Pastaza, Morona Santiago, and Zamora Chinchipe of the Ecuadorian Amazon region to conduct a human health risk assessment. Significant differences in Hg levels were found between provinces, but concentrations were below MPL imposed by Ecuadorian regulations everywhere. Nevertheless, a worrisome picture emerges, especially with regard to the most vulnerable receptors represented by the child population. There are multiple factors of incidence that may affect the possible future development of the phenomenon, and with reference to the social, economic, and environmental context of the region, it can be concluded that it may be appropriate to plan further investigation to arrive at a more comprehensive assessment. The results of this study can be used by decision makers to plan further investigation and to implement monitoring networks, risk mitigation strategies, and groundwater protection measures.