Abstract Soil amendment with manure compost may influence environmental behaviors and bioavailability of toxic organic chemicals ( e.g. pesticide and polycyclic aromatic hydrocarbons). Dynamic parameters like adsorption, kinetics, mobility and degradation of pesticides have been intensively investigated. However, the current methods to evaluate the ultimate real bioavailability of pesticides to crops using physiochemical or biological approaches are limited. In this study, we developed a set of comprehensive and cost-effective parameters relevant to crop response to prometryne (s-triazine herbicide) to assess the accumulation and genotoxicity of the pesticide. Wheat plants exposed to 8 mg kg −1 prometryne for 10 d showed stunt growth, reduced chlorophyll content and damaged membrane lipid. Concomitant treatment with 5% pig manure compost (PMC) alleviated the toxic effect on the plant. Prometryne in soils was readily accumulated by wheat. However, such an accumulation was significantly inhibited by PMC application. Because excessively accumulated prometryne triggered oxidative damage to plants, the biochemical responses of several antioxidant enzymes along with their molecular expressions were determined. In most cases, the activities and transcriptional expression of the enzymes were activated upon the exposure to prometryne but the process was prevented by PMC application. The set of biological parameters tested in this study were very sensitive and cost-effective, and therefore can be used to evaluate the degree of pesticide contamination to plants and other organisms.