It's a key step to estimate the nutrient reference condition of lakes for their nutrient criteria development. A new method was established to calculate the lake nutrient reference condition based the generally extreme statistical theory in the paper. The deficiencies, which lead to artificial error by grouping observed values and difficulty to do statistical inference and reliability evaluation in descriptive statistical methods, taking the frequency analysis as an example, can be overcome. The confidence intervals of parameters and substance concentrations can be obtained by this new method. This method was applied to estimate the reference conditions of Taihu Lake. The calculated results on total nitrogen (TN), total phosphorus (TP) and chlorophyll a (Chl-a) observed by two sites located in the central of Taihu Lake show that the negative minima data of every year fit the generally extreme statistical model well and the feasibility of the approach has been verified. The 25th percentile was recommended as reference conditions. Thus, values of reference conditions show that TN is 0.71 mg x L(-1), TP is 0.025 mg x L(-1) and Chl-a is 1.81 microg x L(-1). The 95% confidence intervals of each measurement was also obtained.