Abstract: It has been discovered that low-head dam could impact local habitat conditions, and alter fish assemblages in streams. However, how fish assemblages respond to the size and function of low-head dams is still not clear. Based on the data collected from 15 impounding segments upstream and 15 plunging areas downstream of low-head dams in the Wannan Mountains at July and November 2016, respectively, we examined how habitat factors and fish assemblages varied seasonally, and the differences in their response to dam size and function. Furtherly, after classifying the collected samples into two types (indigenous species and native-invasive species), we determined whether the indigenous fishes and native-invasive fishes were different in their responses to dam disturbance. A total of 24 fish species representing four orders and ten families were collected, including 11 indigenous species and 13 native-invasive species. Although fish assemblages in the plunging areas did not vary seasonally, the assemblages in the impounding areas was significantly different between July and November, where fishes were more abundant in November than in July. Only the assemblage structure of native-invasive fishes in the plunging areas was influenced by dam size. However, both native fish assemblages in the impounding areas and native-invasive fish assemblages in the plunging areas showed difference in their response to the between-dam-function, suggesting that dam function was more important in impacting fish assemblages than dam size. Compared to those associated with the impounding dams, the irrigating dams had less Zacco platypus but more Cobitis sinensis and Ctenogobius spp. in the impounding areas, and more Rhodeus ocellatus and Misgurnus anguillicaudatus in the plunging areas. In addition, the response of the whole fish assemblages (including both indigenous and native-invasive species) to dam disturbance was similar to the indigenous fish assemblages, instead of the native-invasive fish assemblages. Our results suggest that, in this study area, dam function was more important in influencing local fish assemblages than dam size. Due to their potential differences in response to dam disturbance for the indigenous species and native-invasive species, it is necessary for us to distinguish these two types of species when we assess how anthropogenic activities affect fish diversity in streams.