Native and non-native aquatic plants could have different responses to environmental alterations in riverine systems. It is important to understand the differences in distributions of native and non-native aquatic plants for developing conservation and management strategies of aquatic plants in riverine systems. We monitored the environmental DNA (eDNA) concentrations of the non-native macrophyte Elodea nuttallii and native macrophyte Hydrilla verticillata in the Gonokawa River, Japan in March-October 2021 to estimate the spatiotemporal abundance patterns of the two species. We also examined the eDNA concentrations of each species along the distance from the Haji Dam because the discharge fluctuation in the river segment tended to increase with the distance from the dam. Our results indicated that both species had similar seasonal eDNA dynamics (i.e., peaked in the growing season) in the system; however, the spatial patterns differed between the two species. The eDNA concentrations of the non-native macrophyte tended to have negative relationships with the distance from the dam. In contrast, the eDNA concentrations of the native macrophyte were not correlated with the distance from the dam. These results suggest that effects of flow alteration by the dam may differ between the native and non-native aquatic plants in the system.