The Amazon is a hotspot for mercury (Hg) contamination and the Terra do Meio region, despite its protected status for sustainable use, has never been monitored for this element and might be affected. Looking to address this gap, this study aimed to quantify capillary mercury concentration in riverine populations of Terra do Meio (Xingu Basin, Central Amazon, Brazil) and associated factors with high Hg concentration levels (90 percentile). Hair samples from 182 individuals from Iriri, Riozinho do Anfrísio and Xingu Extractive Reserves (RESEX), aged between 18 and 70 years old, were collected to measure total mercury levels (HgT) and socioeconomic, demographic, and clinical-epidemiological data were annotated. Overall, high concentration levels of Hg were observed with significant differences between localities. Among the factors related to high capillary mercury concentration levels, gender (male), smoking habit, work with agriculture, livestock or extractivism and living at Iriri and Riozinho do Anfrísio RESEX were highlighted. A high prevalence of symptoms related to mercury intoxication, including anxiety, memory deficit, and lower limb problems, was observed. Overall, the results reveal that communities in these RESEXs are exposed to Hg and appear to be suffering from chronic health effects. Considering the increased anthropic alterations observed recently in the Amazon region and the subsequent amplified environmental bioavailability of mercury, further studies and mitigating actions are critical.