This study investigated the distribution of heavy metals in agricultural soils in the vicinity of three large mining landfills of the Kizhnica mine in the Republic of Kosovo. The mining sector is one of the most important sectors of Kosovo’s economic development, and the Kizhnica mine is one of the most important ore producers in Kosovo. Besides the positive aspects, the development of production also has some negative side effects, such as the generation of industrial waste and the possible contamination of surrounding areas, including agricultural land. Therefore, ten sampling sites were selected in the vicinity of the Kizhnica mine. These sites were characterized and assessed as the most important due to the anthropogenic impact of mineral processing and open-tailing waste deposits in Kizhnica. The concentration of Pb, Zn, Cu, As, Cd, Ni, Mn and Sb in the selected samples was determined using inductively coupled plasma–optical emission spectrometry. The data obtained were used to create geochemical maps and calculate the contamination factor, pollution load index and geoaccumulation index. Cluster analysis, Pearson correlation coefficient and air spatial distribution patterns using the air dispersion model were used to evaluate within the area. The results showed that heavy metal levels are influenced by the anthropogenic nature of pollution, confirming a current ecological threat from mining activities in the region. In order to improve waste management, reduce the hazardous impacts of mining and contribute to the sustainable development of the region, the potential reuse of the deposited waste material in the construction industry is proposed.