This study demonstrates an investigation into nanomineralogical and geochemical evolution for the detection of hazardous elements from old, abandoned coal mining deposits capable of causing negative environmental impacts. The general objective of this study is to evaluate the number of nanoparticulate chemical elements in sediments collected during the years 2017 and 2022 from deactivated coal mining areas in the La Guajíra and Cesar regions of Colombia. Sediments were collected and analyzed from areas that experienced spontaneous coal combustion (SCC). The analysis consisted of traditional mineralogical analysis by X-ray diffraction and Raman spectroscopy, nanomineralogy by field emission scanning electron microscope-FE-SEM, and high-resolution transmission electron microscope-HR-TEM (energy dispersive X-ray microanalysis system-EDS). The analyzed sediment samples contained high proportions of amorphous materials containing the chemical elements As, Cl, Hg, Mo, Pb, Sb, and Se. This study emphasizes the need to implement environmental recovery projects at former, now abandoned coal extraction areas located in the investigated region, as they have negative effects on the environment and human health across large regions.