Phytotoxins are produced in plants including agricultural crops. Lupins and other plants of the Fabaceae family produce toxic alkaloids. These alkaloids have been studied in food and feed, however, the environmental fate of alkaloids produced by cultivated lupins is largely unknown. Therefore, we conducted an agricultural field experiment to investigate the occurrence of indole and quinolizidine alkaloids in lupin plant tissues, soil, soil pore water and in drainage water. During the field experiment, alkaloids were regularly quantified (median concentrations) in lupin (13–8.7 × 10³ ng/g dry weight (dw)), and topsoils at depth 0–5 cm (0.1–10 ng/g dw), and depth 15–30 cm (0.2–8.5 ng/g dw), soil pore water (0.2–7.5 ng/L) and drainage water samples (0.4–18 ng/L). Lupanine was the dominant alkaloid in all collected samples. Cumulative amounts of alkaloids emitted via drainage water were around 0.1–11 mg/ha for individual alkaloids over one growing season. The total cumulative amount of alkaloid in drainage water was 14 mg/ha, which is a very small amount compared to the mass of alkaloid in the lupin biomass (11 kg/ha) and soil (0.02 kg/ha). Nearly half of the alkaloids were exported in the drainage water during high flow events, indicating that alkaloids transport preferentially via macropores. These findings indicate that drainage from lupin cultivated areas contribute to surface water contamination. The environmental and ecotoxicological relevance of alkaloids as newly identified aquatic micropollutants in areas with agricultural activities have yet to be assessed.