The safety of drinking water source directly affects human health. Ensuring the safety of drinking water is critical. Microcystin-LR (MC-LR), a toxic and common pollutant, releases by algae into drinking water source and can impede the in-situ remediation effect of aquatic plant on drinking water source purification. However, the effect mechanism of the MC-LR on the purification of the drinking water by aquatic plant remains unclear. This study aims to explore the effects mechanism of MC-LR (0–10 µg L− 1) on drinking water source purification by Hydrocharis dubia (Bl.) backer. After an exposure experiment, the removal rate of NH4+-N, TP, and COD promoted significantly at low concentrations of MC-LR (< 1µg L− 1). And the removal rate of NH4+-N, TP, and COD increased from 78.9–90.7%, 70.0–93.2%, and 46.0–77.3%, respectively. With the increase of MC-LR concentration, the pollutant removal rate was obviously inhibited causing by concentration-dependent. Furthermore, the growth and development of the Hydrocharis dubia (Bl.) backer roots were significantly promoted at the concentration of 0.2 µg L− 1. The length, tips, surface area, and average diameter of the root increased by 71.3%, 271.4%, 265.5%, and 113.0%, respectively. Chlorophyll contents under low-concentration MC-LR shows a 14.5%-15.7% promoting effect compared with the control group (CK). The activities of POD and CAT were also stimulated with the MC-LR increasing at low concentration. Notably, the MDA contents increased with increasing MC-LR concentration (p < 0.01). Therefore, the presence of MC-LR could affect the purification efficiency of Hydrocharis dubia (Bl.) backer in drinking water source. This study indicates the effect mechanism of MC-LR on drinking source water purification by Hydrocharis dubia (Bl.) backer.