Identifying the patterns of how stream fish assemblages vary spatially and how environmental factors influence fish assemblages is critical for fish species conservation and management. We evaluated the spatial patterns in fish assemblages at a river-network scale and documented the correlations between fish assemblages and local habitat features and tributary spatial position using data collected from 94 segments within headwater streams (1st-, 2nd-, and 3rd-order streams) of the Wanhe watershed at Dabie Mountain during July and August 2013. A total of 6 288 specimens representing 42 species, 13 families and 4 orders were collected, among which species of the family Cyprinidae comprised 52.38% of total species richness. Both local habitat (i.e., canopy cover, water temperature, conductivity, substrate size, and heterogeneity) and spatial position variables (i.e., stream order, link, downstream link, and confluence link) varied significantly with a decline in elevation. We observed significant variation in fish diversity, but not abundance, among the 1st-, 2nd-, and 3rd-order streams with higher species richness occurring in higher ordered streams. However, there was no variation in species richness and abundance among the three tributaries (i.e., the Changhe, Wanshui, and Qianshui streams). Both habitat (i.e., elevation) and spatial variables (i.e., stream order and downstream link) had a significant influence on fish species richness, but fish abundance was only influenced by local habitat (i.e., elevation). There was substantial overlap in assemblage structures across the three ordered streams, and an obvious nested pattern was observed for assemblage structures from 3rd-order to 1st-order streams in turn. Additionally, fish assemblage structures were affected by both habitat (i.e., elevation) and spatial variables (i.e., confluence and downstream links). Our results suggest that local fish assemblages in the headwater streams of the Wanhe watershed are determined by both local and spatial processes. Thus, both local habitat conditions and river-network connectivity should be considered in combination when framing schemes for the conservation and management of fish species in this study area.