Hair mercury (HHg) concentration is a biomarker of exposure that is widely used to assess environmental contamination by fish methylmercury and neurodevelopment in children. In the Rio Madeira basin (Brazilian Amazon), total HHg concentrations in 649 mother-infant pairs were measured at birth (prenatal exposure) and after 6 months of exclusive breastfeeding; these mother-infant pairs were from high fish-eating communities (urban, n = 232; rural, n = 35; and Riverine, n = 262) and low fish-eating tin-miner settlers (n = 120). Differences in kinetics were seen between Hg exposure from fish consumption and environmental exposure to a tin-ore mining environment. Overall maternal HHg concentrations (at childbirth and after 6 months of lactation) were higher than those of infant HHg. However, the relative change in HHg after 6 months of lactation showed that mothers decreased HHg while infants increased HHg. The relative change showed a consistently higher increase for girls than boys with a statistical significance only in high fish-eating mothers. The correlation coefficients between maternal and newborn hair were high and statistically significant for mothers living in urban (r = 0.66, p < 0.001), rural (r = 0.89, p < 0.001), and Riverine (r = 0.89, p < 0.001) communities not for tin miner settlers (r = 0.07, p = 0.427). After 6 months of exclusive breastfeeding, correlation coefficients showed high correlation coefficients and statistical significance for all groups (urban, r = 0.73, p < 0.001; rural, r = 0.88, p < 0.001; Riverine, r = 0.91, p < 0.001) except for Tin miners (r = -0.07, p = 0.428). A linear model analysis was used to assess the longitudinal associations of maternal total HHg and total HHg at birth (0 days) and 6 months of age in exclusively breastfed infants. Regression analysis significantly predicted HHg in newborn from maternal HHg for high fish-eating maternal-infant pairs. The concentration of mercury accumulated in newborn tissues (in utero and during breastfeeding) relevant to both, maternal sources and infant exposure, can be reliably assessed from maternal hair.