A heterogeneous photocatalyst, ZnO/reduced graphene oxide (ZnO/rGO or ZG), was synthesised for the photocatalytic degradation of metalaxyl (MX) in aqueous solutions under UV irradiation. The characteristics of the prepared catalyst were determined by FTIR, XRD, FE-SEM, EDS, and BET analyses. The effect of various parameters such as solution pH, catalyst concentration, rGO loading in the catalyst structure, MX concentration and UV light intensity on the photodegradation of MX was investigated. The concentration of MX and the toxicity of the intermediates were determined by HPLC and the Daphnia Magna toxicity test, respectively. The effect of the water anions and radical scavenger compounds on the MX removal process was studied as well. The rate of mineralisation was determined by measuring the total organic carbon (TOC) value using the TOC analyser. The efficiency of the degradation process was compared with the real sample of agricultural drainage and deionised water. At optimum conditions (pH = 7, catalyst loading = 10%, catalyst concentration = 0.75 g/l, MX concentration = 10 mg/l, and UV intensity = 220 MW/cm²), the removal and mineralisation rates were 90.25% and 51.17% after 120 min, respectively. Reactive species scavenging experiments showed that the hole was the most effective factor for MX degradation in the ZG/UV process. The MX degradation rate in real agricultural run-off samples showed that the degradation efficiency was 50.42%, which was significantly lower than that of the synthetic samples. The toxicity bioassay by D. Magna indicated that the toxicity of MX was reduced from 51.22 to 15.17 after 96 h during the ZnO/rGO process. The photocatalytic efficiency decreased in the presence of phosphate and nitrate ions but did not change much in the presence of other water anions. Thus, the ZG/UV process can be effectively used for the degradation of organic pollutants, especially pesticides in wastewater.