The aim of this study was to analyze the effects of roundup and malathion in environmentally relevant and subtoxic concentrations on the metabolic processes of zebrafish Danio rerio. Pesticide toxicity was assessed by changes in the activity of enzymes catalase, succinate dehydrogenase, glutathione transferase, glutathione reductase, protein phosphatase and caspase 3. Roundup has been shown to activate catalase, protein phosphatase, and caspase-3, whereas malathion induces caspase 3 only. At the same time, the studied organophosphate pesticides caused a significant decrease in glutathione transferase and succinate dehydrogenase compared to the control, especially under the action of malathion. Moreover, under the influence of malathion there was a decrease in the activity of protein phosphatase and catalase. As for glutathione reductase, the subtoxic concentration of roundup caused its activation, and the ecologically real concentration of malathion caused its inhibition. In sum, malathion caused more noticeable toxic effects in zebrafish than roundup. Therefore, organophosphate pesticides carry significant risks of toxic effects on fish as non-target organisms, which is important to consider when choosing agronomic maintenance options for the harvest and the potential danger to the environment.