In line with the 1000-day initiative and the Sustainable Development Goals (SDG) 2 and 3, we present a cross-sectional analysis of maternal health, infant nutrition, and methylmercury exposure within hard-to-reach indigenous communities in the state of Pará, Brazilian Amazon. We collected data from all women of childbearing age (i.e., 12–49) and their infants under two years old in three Munduruku communities (Sawré Muybu, Sawré Aboy, and Poxo Muybu) along the Tapajos River. We explored health outcomes through interviews, vaccine coverage and clinical assessment, and determined baseline hair methylmercury (H-Hg) levels. Hemoglobin, infant growth (Anthropometric Z scores) and neurodevelopment tests results were collected. We found that 62% of women of childbearing age exceeded the reference limit of 6.0 μg/g H-Hg (median = 7.115, IQR = 4.678), with the worst affected community (Sawré Aboy) registering an average H-Hg concentration of 12.67 μg/g. Half of infants aged under 24 months presented with anemia. Three of 16 (18.8%) infants presented H-Hg levels above 6.0 µg/g (median: 3.88; IQR = 3.05). Four of the 16 infants were found to be stunted and 38% of women overweight, evidencing possible nutritional transition. No infant presented with appropriate vaccination coverage for their age. These communities presented with an estimated Infant Mortality Rate (IMR) of 86.7/1000 live births. The highest H-Hg level (19.6 µg/g) was recorded in an 11-month-old girl who was found to have gross motor delay and anemia. This already vulnerable indigenous Munduruku community presents with undernutrition and a high prevalence of chronic methylmercury exposure in women of childbearing age. This dual public health crisis in the context of wider health inequalities has the potential to compromise the development, health and survival of the developing fetus and infant in the first two critical years of life. We encourage culturally sensitive intervention and further research to focus efforts.