Fish has great socioeconomic, cultural, and nutritional importance for Amazonian populations. Despite all health benefits, fish can accumulate great amounts of mercury (Hg). The entry of Hg in aquatic trophic chains is an issue of concern to animal and human health. Higher risks of human exposure are strongly related to fish consumption. Upper Solimões population has one of the highest fish consumption rates of the Amazon. This study aimed to access the concentration of total Hg (THg) in muscle, liver, and gills of 17 species of fishes marketed in the Upper Solimões Region and Health Risk Assessment. Higher concentrations were observed in Carnivores/Piscivores. The highest THg concentration was found in liver of Cichla ocellaris (4.549 μg/g) and the lowest in gills of Hoplosternum littorale (0.002 μg/g). Most species had higher THg concentrations in muscle>liver>gills, in the Ebb period, and liver>muscle>gills, in the Flood period. Hoplias malabaricus, Pseudoplatystoma fasciatum, Plagioscion squamosissimus, Ageneiosus inermis, and C. ocellaris presented average THg concentrations above the safe limit stablished by WHO. THg levels in C. ocellaris, H. malabaricus, P. squamosissimus, P. fasciatum, and Semaprochilodus insignis were higher than those found in fish of heavily impacted areas. Signs of bioaccumulation and biomagnifications of Hg can already be observed in this region. The Western Amazon Region urgently needs government actions to inhibit Hg release in aquatic ecosystems and to advise this population on the safe amount of fish to be eaten according to species and period of the year.