Background: A large number of chemicals are constantly introduced to surface water from anthropogenic and natural sources. So far, unlike anthropogenic pollutants, naturally occurring compounds are not included in environmental monitoring programs due to limited knowledge on their occurrence and effects in the environment. Since previous studies suggest that natural compounds might contribute to mixture risks in aquatic ecosystems and for drinking water production, there is a need to increase empirical evidence on the occurrence of these compounds in aquatic systems. To this end, we performed target screening on 160 toxic secondary plant metabolites (PSMs), prioritized in silico for their likelihood of occurrence, persistence, toxicity and mobility in river waters, using liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS). The samples were collected during rain events from three Danish rivers from an area covered by grassland, forest and agricultural crops. Results: In total, 27 targets belonging to different compound classes such as alkaloids, coumarins and flavonoids were detected, among them 12 compounds, which have not been reported in surface waters before. The most prominent compound class was the group of alkaloids with 41% of the detected targets, many of them detected in more than 80% of the samples. Individual compound concentrations were up to several hundred ng/L with the neurotoxic alkaloid coniine from poison hemlock and the flavonoid daidzein reaching maximum concentrations of about 400 and 282 ng/L, respectively. In some samples, especially from Vejle river, the rise in concentration of target compounds were associated with increase in the rain intensity and elevated water table in the river. Conclusions: The measured natural toxin concentrations are well within the range of those of synthetic environmental contaminants and need to be considered for the assessment of potential risks on aquatic organisms and drinking water production. © 2021, The Author(s).