Manganese (Mn) is an abundant element in terrestrial and coastal ecosystems and an essential micronutrient in the metabolic processes of plants and animals. Mn is generally not considered a potentially toxic element due to its low content in both soil and water. However, in coastal ecosystems, the Mn dynamic (commonly associated with the Fe cycle) is mostly controlled by redox processes. Here, we assessed the potential contamination of the Rio Doce estuary (SE Brazil) by Mn after the world’s largest mine tailings dam collapse, potentially resulting in chronic exposure to local wildlife and humans. Estuarine soils, water, and fish were collected and analyzed seven days after the arrival of the tailings in 2015 and again two years after the dam collapse in 2017. Using a suite of solid-phase analyses including X-ray absorption spectroscopy and sequential extractions, our results indicated that a large quantity of Mn
II
arrived in the estuary in 2015 bound to Fe oxyhydroxides. Over time, dissolved Mn and Fe were released from soils when Fe
III
oxyhydroxides underwent reductive dissolution. Due to seasonal redox oscillations, both Fe and Mn were then re-oxidized to Fe
III
, Mn
III
, and Mn
IV
and re-precipitated as poorly crystalline Fe oxyhydroxides and poorly crystalline Mn oxides. In 2017, redox conditions (Eh: −47 ± 83 mV; pH: 6.7 ± 0.5) favorable to both Fe and Mn reduction led to an increase (~880%) of dissolved Mn (average for 2015: 66 ± 130 μg L
−1
; 2017: 582 ± 626 μg L
−1
) in water and a decrease (~75%, 2015: 547 ± 498 mg kg
−1
; 2017: 135 ± 80 mg kg
−1
) in the total Mn content in soils. The crystalline Fe oxyhydroxides content significantly decreased while the fraction of poorly ordered Fe oxides increased in the soils limiting the role of Fe in Mn retention. The high concentration of dissolved Mn found within the estuary two years after the arrival of mine tailings indicates a possible chronic contamination scenario, which is supported by the high levels of Mn in two species of fish living in the estuary. Our work suggests a high risk to estuarine biota and human health due to the rapid Fe and Mn biogeochemical dynamic within the impacted estuary.