The primary sources and the conditions for the formation of the Paleogene–Neogene coal-bearing deposits in the Zeya–Bureya sedimentary basin were identified and studied with the help of paleogeographic reconstructions and geochemical analyses. Based on the results obtained, we suggest a new basic model of element transfer into the coal, involving two mutually complementary processes to account for the introduction and concentration of gold and other trace elements in the sequences investigated. The first process reflects the system in which peatlands were concentrated along the basin’s junction zone and the passive internal residual mountain ranges. The second reflects the junction’s contrast-type (sharp-type) forms conditions along the external mobile mountain-fold frame. The eroded gold particles were transported over 10–20 km as complex compounds, colloids, dispersed particles, and nanoparticles, and remobilized into clastogenic and dissolved forms along the first few kilometers. The release of gold in the primary sources occurred due to weathering of gold-bearing ore zones, followed by transportation of gold by minor rivers to the areas of peat accumulation. This study considered the probability of the accumulation of high concentrations of gold and rare earth elements (REE) in coal due to the introduction of organic and inorganic materials during floods, with episodes of catastrophic events, and volcano–hydrothermal activities.