Human exposure to mercury is a leading public health problem. Artisanal and small-scale gold mining (ASGM) is a major source of global mercury emissions. Although occupational mercury exposure to miners (via mercury vapor inhalation) is known, chronic mercury exposure to nearby residents that are not miners (via mercury-contaminated fish consumption) is poorly characterized. We conducted a population-based mercury exposure assessment in 23 communities (19 rural, 4 urban) around the Amarakaeri Communal Reserve, which is bordered on the east by heavy ASGM activity. We measured total mercury in hair (N = 2083) and blood (N = 476) from March-June 2015 and performed follow-up measurements (N = 723 hair and N = 290 blood) from February-April 2016. Mercury exposure risk was highest in communities classified as indigenous, or native, regardless of proximity to mining activity. Residence in a native community (vs. non-native) was associated with mercury levels 1.9 times higher in hair (median native 3.5 ppm vs. median non-native 1.4 ppm total mercury) and 1.6 times higher in blood (median native 7.4 ng/mL vs median non-native 3.2 ng/mL total mercury). Unexpectedly, proximity to mining was not associated with exposure risk. These findings challenge common assumptions about mercury exposure patterns and emphasize the importance of population-representative studies to identify high risk sub-populations.