Abstract: Taking the Hunhe River water system in Liaoning Province of Northeast China as a case, this paper investigated the community structure of periphyton and the physical and chemical characteristics of water environment at 62 sampling sites, and, by using the biological integrity index of periphyton (P-IBI) and the habitat environment quality index (QHEI), a health assessment on the aquatic ecosystem of the water system was conducted. There was a great spatial heterogeneity in the periphyton community structure, and the sampling sites could be divided into 4 groups, with significant differences in the community structure, species richness, density, and Shannon diversity index among the groups. Canonical correspondence analysis (CCA) showed that ammonia nitrogen (NH₄⁺-N) and dissolved phosphorus (PO₄^3--P) were the main water environment factors driving the formation of the periphyton community structure in the water system. The health assessment of the water system based on P-IBI and QHEI was basically in consistency, though the assessment of several reaches had large discrepancy. Overall, the Suzi River at the upper reaches of the water system had a better health status, while the upper reaches of Hunhe River and the main stream of Hunhe River at its middle and lower reaches were worse in health.