The numerous low-head dams constructed across stream ecosystems have increasingly been recognized as significant anthropogenic stressors that disrupt the natural structure and functioning of riverine environments. These small-scale hydraulic structures, while often overlooked in comparison to large dams, can substantially alter hydrological regimes, fragment habitats, and modify sediment and nutrient transport. Although their ecological impacts are less studied, low-head dams may have far-reaching effects, particularly in headwater streams that are ecologically sensitive and often support high biodiversity. In order to better understand the ecological consequences of such modifications, this study focused on evaluating the effects of low-head dams on macroinvertebrate community structure and assembly processes in headwater streams located in the mountainous region of southern Anhui Province, China. A field investigation was carried out in November 2021, during which macroinvertebrate samples were collected from three types of stream sections: natural reference reaches, downstream scouring zones directly impacted by dam outflows, and upstream impoundment zones characterized by slower flow and sediment accumulation. A total of 199 macroinvertebrate taxa were identified, encompassing 5 phyla, 9 classes, 19 orders, 90 families, and 188 genera. Of these, 125 taxa were found in the reference reaches, 95 taxa in scouring zones, and 77 taxa in impoundment zones. Overall, macroinvertebrate density and biomass were significantly higher in the reference sites, while pollution-tolerant taxa showed greater abundance and biomass in the dam-influenced zones, indicating degraded water quality and simplified habitat structure. Non-metric multidimensional scaling (NMDS) analysis revealed distinct community composition patterns among the three site types, with significant dissimilarities between reference sites and both downstream and upstream zones. Redundancy analysis (RDA) further identified key environmental drivers of community variation, including electrical conductivity, river width, and substrate composition—particularly the presence of bedrock and cobble. These variables were closely associated with dam-induced habitat modifications, such as reduced flow velocity, increased sedimentation, and changes in substrate heterogeneity. Variation partitioning analysis demonstrated that dam disturbance altered the dominant mechanisms underlying community assembly. While environmental filtering was the primary driver in the undisturbed reference sites, spatial processes, such as dispersal limitation and habitat isolation, became more prominent in the dam-affected zones. This shift suggests that low-head dams not only modify local habitat conditions but also disrupt longitudinal connectivity, leading to reduced species exchange and altered biodiversity patterns across spatial scales. These findings provide important ecological insights into how even small dams can reshape aquatic communities and ecosystem functioning in headwater streams. They highlight the vulnerability of these ecosystems to anthropogenic fragmentation and stress the importance of considering the cumulative impacts of numerous small hydraulic structures in regional water management. The results underscore the need to incorporate the impacts of low-head dams into river monitoring, biodiversity conservation planning, and ecological restoration strategies in mountainous freshwater systems, where the protection of ecological integrity is essential.