Researchers recognize the silent, negative and deleterious effects caused by mercury pollution in gold mining areas. Freshwater turtles are culturally part of the diet of riverside populations in the Amazon region and this area presents mercury (Hg) pollution issues mainly due to gold mining activities. Thus, this research aimed to evaluate the total mercury (THg) content in the different organs of Amazonian giant river turtle (Podocnemis expansa) and carry out a human health risk assessment associated with the consumption of these animals. This study was conducted in the Vila Balbina, municipality of Presidente Figueiredo, state of Amazonas, Brazil. Skin (n = 28), muscle (n = 19) and brain (n = 2) samples were analyzed by Atomic Absorption Spectrometry (TDA-AAS) and a DMA-80™ mercury analyzer was used for the total mercury determinations. The average values found for THg in the skin, muscle and brain samples were, respectively, 0.1045 mg·kg−1, 0.1092 mg·kg−1 and 0.0601 mg·kg−1. Thus, THg was observed even though the P. expansa were kept in captivity, possibly due to previous contamination by air, water and food. The Hazard Quotient (HQ) was calculated considering a 9.07 g·day−1 intake dose of P. expansa and the consumption of turtles once a week showed an HQ = 2.45, which may cause long-term injuries to human health. Although the muscle concentrations were below the maximum limit established by the World Health Organization (WHO) and Brazilian regulatory agencies, it is important to evaluate consumption factors such as amount ingested, frequency and animal gender, which may cause a potential risk to regular consumers due to mercury bioaccumulation. The WHO may consider various aspects in order to warn the Amazon population about the severity and silent hazard of this metal, especially due to the importance of this matrix in the region. This region urgently needs government actions to inhibit clandestine mining and to prevent future serious, chronic health problems of the entire population.