Stream ecosystems are of significant ecological value due to their rich aquatic biodiversity and specificity, yet they are also highly vulnerable and urgently require more attention and protection. Zooplankton, as an important component of the aquatic food web, has long been overlooked in terms of its functional role in stream ecosystems. To investigate the role of zooplankton in stream ecosystems, this study focused on the headwaters of the Chishui River, a basin with minimal human impact and conducted a comparative analysis of the taxonomic and functional groups characteristics of zooplankton under two distinct hydrological conditions: the dry season (December) and the wet season (May). The relationships between these characteristics and water environmental factors were also examined. A total of 29 zooplankton species were identified. The number of species identified in the dry season (24 species) was twice that in the wet season (12 species). Compared to other water body types, the density of stream zooplankton was extremely low, ranging from 0.02 to 4.9 ind./L. Based on functional traits such as habitat preference, body size, and feeding habits, the taxonomic groups were classified into 11 functional groups. The occasional planktonic benthic scraper (SS), the small to medium-sized predator with swimming ability (SP), and the small filter-feeder (SCC) dominate the functional groups， and they all reflect functional adaptation strategies to turbulent habitats. This study report that the proportion of the benthic scraper group (SS) in the total functional groups in the stream can increase sharply from 17.7% in the dry season to 68.4% in the wet season, demonstrating a sensitive indicative characteristic in response to hydrological shifts. Furthermore, Mantel tests revealed that the composition of functional groups was significantly correlated with various environmental factors, including phytoplankton cell density, water temperature, pH, oxidation-reduction potential (ORP), total phosphorus (TP), and ammonium nitrogen (NH??-N), indicating that functional groups are more sensitive environmental indicators than taxonomic groups. The study demonstrates that the classification of functional groups can integrate species with similar ecological niches, thereby effectively compensating for the limitations of taxonomic groups in assessing the standing stock of stream zooplankton. This provides a new theoretical perspective for constructing diagnostic indicator systems for stream ecological health.