This study represents the first application of Fe-citrate-based photo-Fenton chemistry for the degradation of chlorpyrifos (CPF) spiked into agricultural runoff, and its phytotoxicity assessment. The effects of the initial CPF concentration, time and ratio of Fe-citrate/H2O2 on CPF removal during the photo-Fenton reaction were investigated and modeled with analysis of variance using R software by the response-surface methodology package. According to the stationary point in original units, the optimal condition for 70.00% CPF removal was as follows: CPF = 2.5 mg L-1 (0.0), time = 48.0 min (0.585) and Fe-citrate/H2O2 = 0.075 (0.539). Beside running the system at near-neutral pH, another strength of this study is related to the treatment of agricultural runoff contaminated with CPF with a raceway pond reactor, which has the advantages of simplicity of the facilities and procedures, as well as the possibility of using sunlight more efficiently in the field of applications. Finally, untreated and treated agriculture runoffs were used as irrigation to determine their phytotoxic effects on seed germination of cress (Lepidium sativum). Solar photo-Fenton treatment greatly reduced phytotoxicity of agriculture runoff and showed the highest germination percentage (70%) compared to both raw agricultural runoff (60%) and untreated CPF-spiked runoff (35%).