A new method, with the non-fully mixed coefficient (NFMC) considered, was put forward to calculate the water environmental carrying capacity (WECC) for huge river-connected lakes, of which the hydrological conditions always vary widely during a year. Poyang Lake, the most typical river-connected lake and the largest freshwater lake in China, was selected as the research area. Based on field investigations and numerical simulation, the monthly pollutant degradation coefficients and non-fully mixed coefficients of different lake regions were determined to explore the WECCs of COD, TN and TP of Poyang Lake in a common water year. It was found that under the hydrological conditions of a common water year the total WECCs of COD, TN and TP in the lake were respectively 181.9 × 104 t, 33.3 × 104 t and 1.86 × 104 t. Due to the varied lake water volume and self-purification ability, an evident temporal fluctuation of WECCs in Poyang Lake was observed. The dry seasons were characterized by a higher NFMCs but lower WECCs owing to the lower water level and degradation ability. Variation coefficients of COD and TN WECC were close to each other, of which the average level was about 58.5%, a little higher than that of TP.