•Total Hg and MeHg in blood, hair, and feces were studied in subsistence Amazon communities.•Mean fish consumption rate is 146.6 g.day−1 (men, women, and children) in the most remote village.•Women and children excrete THg in feces in comparable concentrations.•Mother`s hair-Hg concentration is a good predictor of children’s hair-Hg.•Women median hair:blood Hg ratio in adult villagers is 269. The Madeira River (Amazon Basin) has been impacted by activities related to artisanal and small-scale gold mining (ASGM), deforestation and burning (for timber, agriculture, and hydroelectric dam projects). All these activities contribute to environmental mercury (Hg) release and cycling into the Amazon ecosystem and thus to changing lifestyles. We assessed exposure to total and MeHg in two small riverine communities of the Madeira River (Amazon): Lago Puruzinho (LP, n = 26 families) and São Sebastião do Tapurú (SST, n = 31 families). Samples of human hair (n = 137), blood (n = 39), and feces (n = 41) were collected from adults and children (0–15 years of age). In women of childbearing age from LP village, the mean blood total-Hg (THg) (45.54 ± 24.76 μg.L−1) and MeHg (10.79 ± 4.36 μg.L−1) concentrations were significantly (p = 0.0024; p < 0.0001, respectively) higher than in women from SST village (THg: 25.32 ± 16.75 μg.L−1; MeHg: 2.32 ± 1.56 μg.L−1) village; the trend in hair-Hg persisted but was statistically significant (p < 0.0145) only for THg (LP, 11.34 ± 5.03 μg. g−1; SST, 7.97 ± 3.51 μg. g−1). In women, the median hair:blood ratio of total Hg was 269. In children, the mean hair THg concentrations were 6.07 ± 3.60 μg. g−1 and 6.47 ± 4.16 μg. g−1 in LP and SST; thus, not significantly different (p = 0.8006). There was a significant association (p < 0.001) between hair-Hg concentrations of mothers and their respective children. The excretion of Hg in feces of women (0.52 μg. g−1 dw) was not significantly different from children (0.49 μg. g−1 dw). The only statistically significant correlation between Hg in feces and in hair was found in children, (n = 16, rs = 0.38, p = 0.005). Significant relationship was seen between the levels of THg in blood and hair of women from LP and SST. Based on hair-Hg concentrations, fish consumption rate ranged from 94.5 to 212.3 g.day−1. Women and children excrete THg in feces in comparable concentrations. However, the mean fish consumption rate and blood MeHg are higher in the most remote villagers. Mother`s hair-Hg concentration is a good predictor of children’s hair-Hg.