Maintaining sufficient levels of plant nutrients in the soil and controlling certain heavy metals, which can be toxic to the environment, are critical to ensure sustainable agricultural production. The study aimed to assess the linkage of crop-specific agricultural practices established by farmers in the Kvemo Kartli region (Georgia) with metal accumulation in soils of agricultural lands being subject to influence from polluted irrigation water in the past. In particular, we tried to identify the primary sources of micronutrients, including iron (Fe), copper (Cu), manganese (Mn), nickel (Ni), and zinc (Zn), and toxic elements such as cadmium (Cd) and lead (Pb), and share of the contaminated irrigation water and other factors related to agricultural practices under different land uses, such as intensive and extensive arable farming, vineyards, orchards, and permanent pastures having the least disturbed soil. Based on principal component analysis, five primary sources were identified and categorized according to farmers' interviews and previous studies conducted in the region. The results showed that increased concertation of plant-available Cu, Zn, Cd and Pb were mainly associated with irrigation water and intensive use of fungicides; Fe, Mn, and Ni were closely linked to several factors, such as the mineralogical composition of soils, mineral and organic fertilizers inputs, and atmospheric deposition from diffuse sources, where exhausts from transport are probably the primary source. During our study, we attempted to differentiate irrigation water inputs from fungicides using simulation based on irrigation pattern and irrigation water quality on the one hand and fungicide application rate and their metal content on the other. The simulation revealed that the intensive application of fungicides, especially in vineyards, is more significant in enriching soils with Cu and Zn than irrigation water. Identification of factorial dependences was supported by statistical analysis and application of a number of contamination assessment methods: Contamination Factor (CF), Pollution Load Index (PLI), single-factor Pollution Index (PI), Nemerow’s comprehensive pollution index (PIN), Enrichment Factor (EF), and Geo-Accumulation Index (Igeo). Applied environmental indices indicate that the soils under the former and existing vineyards are the most enriched with Cu and Zn, highlighting the significance of agricultural practices on heavy metals accumulation in soils of agricultural lands.