Our study assessed the actual water situation in the estuarine area of Lake Wuli, Meiliang Bay, Lake Taihu, China, based on eutrophication levels and status of water quality using the trophic level index (TLI) and water quality index (WQI) methods. In the wet (August 2017) and dry (March 2018) seasons, 22 estuarine areas were tested at 69 sampling sites, which included lake and rivers. Five parameters—chlorophyll a (Chl-a), total phosphorus (TP), total nitrogen (TN), Secchi disk (SD) and permanganate index (CODMn)—were measured to calculate the TLI, and 15 parameters—temperature (T), pH, electrical conductivity (EC), dissolved oxygen (DO), total dissolved solids (TDS), TN, TP, ammonium (NH4-N), nitrate (NO3-N), nitrite (NO2-N), CODMn, calcium (Ca²⁺), magnesium (Mg²⁺), chloride (Cl⁻) and phosphate (PO4-P)—were measured to calculate the WQI. The average TLI and WQI values in the wet season were 61.69 and 60.70, respectively, and the eutrophication level and water quality status were worse than that in the dry season (TLI: 57.40, WQI: 65.74). Significant differences were observed between three parts of Lake Wuli (West, Middle and East). Regardless of wet or dry season, East Wuli had worse eutrophication levels and water quality status than the other parts, whereas West Wuli showed less severe levels. DO, TN and CODMn used in the minimum WQI (WQImin) were the most effective parameters in our study. WQImin had stricter standards than WQI when analyzing water quality in the estuarine area of Wulihu. Factor analysis from principal component analysis (PCA) indicated that N might be the main factor affecting water quality of the most eastern sites in the wet season, and P may be the main factor in the dry season. Our results provide a valuable contribution to inform decision-making for the management of water environments by providing the actual water situation of the estuarine area of Lake Wuli.