Heavy metal contamination of soils is widespread and induces a long-term risk to ecosystem health. This research focuses on the heavy metal contamination, transfer values and risk assessment in the Kočani Field plant system (Republic of Macedonia). To identify the heavy metal concentrations in Kočani crops (rice and maize), the geochemical analysis was performed by inductive coupled plasma mass spectrometer and thereupon the transfer factor (TF) and estimated daily intake amount values were calculated. The highest As, Cd, Mo, Pb and Zn values were determined in the rice samples grown in the paddy fields near the Zletovska River. The highest Pb and Mo concentrations measured in the maize samples were from the maize fields near the Zletovska River and Ciflik city. High TF values for Mo, Zn, Cd and Cu revealed a strong accumulation of Mo, Zn and Cd by rice and Mo and Zn by maize crops. The results of the estimated daily intake showed that the regular consumption of rice and maize crops containing the highest Cd, Mo, Pb and Zn concentrations could pose a serious threat to human health, because the daily intake of Cd, Mo, Pb and Zn for crops grown in the fields around the Zletovska River exceeded the recommended provisional tolerable daily intake values. Taking into account the results, the area around Zletovska River is considered as the most anthropogenically impacted part of Kočani Field.