Mercury is responsible for serious episodes of environmental pollution throughout the world, especially in the Amazon. This toxicity has led regulatory agencies to focus on fish as the target organism for protecting the health of humans and other sensitive organisms. Unfortunately, in the Amazon area, different sampling strategies and the wide variety of sampling areas and fish species make it extremely difficult to determine relationships across geographic regions or over time to ascertain historical trends. Thus, the aim of this work was to achieve three main objectives: a comparative study of mercury contamination in fish of Itaituba (Tapajós, located downstream of the largest gold-mining region in Amazon) and Belém (an area non-exposed to mercury pollution of anthropogenic origin), perform an analysis of inorganic mercury (IHg) versus monomethylmercury (MeHg) contents, and, finally, compare mercury contamination in Tapajós over time. Five piscivorous species were obtained in Itaituba and Belém. Also, four non-piscivorous species were collected in Itaituba. For the first time, mercury speciation showed that (1) current MeHg levels in piscivorous species in Tapajós are higher than those of the non-exposed area, (2) piscivorous species from Itaituba (dourada, filhote, and sarda) contained mercury levels above the World Health Organization safety limit (~17%) and/or above the US Environmental Protection Agency tissue residue criterion (40%), (3) increased MeHg is usually accompanied by increased IHg, and (4) the mean total mercury concentrations for piscivorous species in Itaituba were within the same range and, associated uncertainties as those previously reported, although a remarkable decreasing trend over time was observed for mean total Hg concentrations in non-piscivorous species from Itaituba. The present study supports the importance of continuous monitoring of both populations in the Amazon Rivers. Our results will better assist the development of preventive strategies and governmental actions to confront the problem of mercury contamination in the Amazon.