Water quality safety is the key factor to maintain the ecosystem service functions of lakes. Field investigations and statistical analyses were carried out to study the water quality of a large, agriculture-stressed lakes (e.g., Chagan Lake) in Northeast China. The hydro-chemical properties of the Chagan Lake are HCO3·CO3-Na. Nutrient (N and P) and non-nutrient (pH and F−) were found to be the major factors that threaten water quality safety of the lake. The concentration of total nitrogen (TN) and total phosphorus (TP) was found to vary seasonally and at different locations. The overall lake water had mean TN and TP values of 2.19 mg/L and 0.49 mg/L, respectively, in summer. TN was the major factor for water quality deterioration in the western region of the lake, while TP was the principal factor in the other regions, as determined by a principal component analysis (PCA). Fluoride (F−) concentration in the lake water were related to the values of total dissolved solid (TDS), pH, and electrical conductivity (EC). In addition, eutrophication is a fundamental index that has been affecting the ecological evaluation of water quality. The results showed that trophic level index (TLI), trophic state index (TSI), and eutrophication index (EI) were evaluated to quantify the risk of eutrophication. However, TLI and TSI can better describe the purification effect of the wetland. These indices showed that the lake water was hyper-eutrophic in summer, with TLI, TSI, and EI values of 60.1, 63.0, and 66.6, respectively. Disparities in water quality were observed among whole areas of the lake. Overall, this study revealed that controlling agriculture drainage is crucial for lake water quality management. The study generated critical data for making water quality management plans to control the risk.