Abstract: The estuary wetlands are important parts of the large-scale shallow lake systems, but the studies on their ecological status is limited. Shibalianwei wetland is a large-scale constructed wetland formed by "Returning Farmland to Wetland" Program. The wetland is located in the estuary area of Nanfei River flowing into Chaohu Lake. To investigate the relationship between water quality parameters and phytoplankton community characteristics, a total of 72 samples were collected from the Shibalianwei wetland in July 2018. The results show that: (1) According to the water quality index, the N and P content of the water bodies are high and in the range of moderate eutrophication level to severe eutrophication level. (2) 119 phytoplankton species, mostly small-sized algae, belonged to 7 phyla and 83 genera were found in the inside wetland with the dominant ones of Merismopedia sp., Aphanocapsa sp., Dictyosphaerium sp., and Crucigenia sp.; Comparatively, 85 species belonged to 63 genera and 7 phyla, mostly large-sized algae, were found in the waters outside the wetland with the dominant ones of Pseudanabaena sp., Aphanizomenon sp. and Microcystis wesenbergii. (3) The average density and biomass of phytoplankton in the inner wetland were 12 780.16×10⁴ L^-1 and 23.65 mg·L^-1, while those in the outer wetland were 5 083.38×10⁴ L^-1 and 7.1 mg·L^-1, respectively. (4) The results of canonical correspondence analysis (CCA) show that total nitrogen, ammonia nitrogen, soluble reactive phosphorus, electrical conductivity, water temperature, transparency, and aquatic plant coverage were significantly correlated with the distribution of phytoplankton (P < 0.05); The results of the multiple regression tree analysis (MRT) show that the phytoplankton communities were significantly different when water transparency was above and below 29 cm. With the water transparency below 29 cm and the threshold of soluble reactive phosphorus (SRP) as 0.045 mg·L^-1, the phytoplankton communities could further be divided into two significantly different clades. Variance decomposition analysis further show that the nutrient concentration in the water column was the main factor affecting phytoplankton community. The results of the study can provide new basic data for further understanding of the wetland ecology in large shallow lakes and the eutrophication management of Lake Chaohu.