A quantitative microbial risk assessment was conducted to assess the health risks associated with the exposure of agricultural workers to tertiary treated wastewater in irrigated fields through soil ingestion in Cyprus. Three pathogenic microorganisms were chosen, particularly E. coli (bacteria), rotavirus (viruses) and Cryptosporidium. Two extreme exposure scenarios were investigated. Monte Carlo simulations were performed using input data from literature, and the model outputs were compared to the health standards of the World Health Organization (WHO). The results suggested that additional treatment is required for all pathogens to satisfy the health standards. Sensitivity analysis identified the source concentration and pathogen reduction due to soil aquifer passage as the most influential factors in the model outputs. Additional computations were performed to evaluate the minimum pathogen reduction due to soil aquifer passage so that the health targets are achieved for the 95 % of the output values. Rotavirus and Cryptosporidium were found to require more treatment than E. coli. The inclusion of these reference pathogens to the monitoring network of the local authorities is recommended, and the role of soil aquifer passage is emphasized on reducing the concentration of the contaminants.