With the possible increase in mining activities and recently projected population growth in Colombia, large quantities of nanoparticles (NPs) and potentially hazardous elements (PHEs) will be of major concern to mine workers, indigenous residents, and surrounding communities. This study highlights the need to regulate the pollution from Colombian mining activities that comply with regional regulations and global strategies. Colombian coal rejects (CRs) from the Cesar Basin, Colombia, were studied primarily by advanced electron microscopic and analytical procedures. Therefore, the goal of this research is to evaluate the role of NPs in the alteration of CRs’ structure in a renewed zone at Cerrejón coal area (La Guajira, Colombia) through advanced electron microscopic (AEMs) methods. The objective of the analysis is to evaluate the incidence mode of nanoparticles, which contain potentially hazardous elements. The bulk crystallography (X-ray diffraction), chemical structure, and morphologies of NPs were studied by high-resolution transmission electron microscopy (HR-TEM), field emission scanning electron microscopy (FE-SEM), micro-beam diffraction (MBD), selected area electron diffraction (SAED), and energy-dispersive X-ray spectroscopy (EDX) procedures. The AEMs provided comprehensive insights into the geochemical evolution of CRs. Consequently, the AEMs can be used as essential tools for CR management in coal mining areas. The regular dimension of detected NPs was found to be above 2 nm. Ultrafine particles of quartz were identified by the advanced electron microscopy. Furthermore, the findings also revealed aluminium, calcium, potassium, titanium, iron oxides, and PHEs in the CRs. The extensive water practice in the coal extraction process combined with atmospheric oxygen supports oxidations of iron sulphide, thus releasing PHEs to the surrounding environment. Dehydration of sulphate salts fluctuate at consistent humidity in the coal mine environments. The study demonstrates the great influence of coal mining activities on the environment and human health.