Abstract: The total nitrogen (TN) and total phosphorus (TP) contents in the lake water are widely used to estimate the eutrophication levels of the lakes. However, the laboratory analyses results might be not always reliable and accurate because the analyses procedures are often affected by many factors, i.e., the storage method, duration and conditions, especially when a large number of water samples need to be analyzed. To the TP and TN content analyses of the lakes that mostly developed in Karst area in Yunnan, especially to the large lakes and remotely located lakes, the long transportation distance and large water sampling numbers make it difficult to complete the analyses in a limited time duration. Considering theses actual situations, we selected the Lake Fuxian, in that with a very low TP and TN contents, the Lake Yangzong with a middle level of TN and TP contents, and also Lake Dian (Dianchi) with a relatively high TN and TP contents, to test how the TN and TP contents, and also the dissolved TN and TP would change when the water samples are transported and stored under low-temperature condition. Then to fix the optimal storage time to complete the laboratory analyses procedures. The test results indicate that: 1. The total nitrogen and phosphorus contents of the water sample that obtained immediately after sample taken from Dianchi is the highest, of which the TN content is 2.44  mg/L, with the dissolved nitrogen content is 1.47 mg/L that accounting for 60% of total nitrogen, and the TP content is 0.13 mg/L, with the dissolved phosphorus content is 0.02 mg/L that accounting for 15% of total phosphorus. To the water samples taken from Lake Yangzong, the TN contents is 0.73 mg/L, with the dissolved nitrogen content is 0.60 mg/L, accounting for 82% of the TN, the TP contents is 0.04 mg/L, with the dissolved phosphorus content is 0.03 mg/L, accounting for 75% of the TP. The water samples taken from Lake Fuxian show the lowest TN and TP contents, with the TN content of 0.32 mg/L and dissolved nitrogen content of 0.28 mg/L, that accounting for 90% of the TN, the TP contents is 0.02mg/L, with the dissolved phosphorus content of 0.01 mg/L, accounting for 50% of the TP. 2. Along with the low-temperature storage duration increase, the TN and TP contents of the water samples decrease. The total nitrogen and total phosphorus contents of the water samples taken from Lake Yangzong and Dianchi decrease more than that from Lake Fuxian. 3. With the filtration pretreatment procedure, the TN and TP contents in the lake water samples taken from Lake Yangzong and Dianchi also show a significant decrease, but the difference is not so much in the water sample taken from Lake Fuxian. Our findings indicate the storage duration exert a stronger impact on the higher eutrophication level lake water than that on the lower eutrophication level lake water.In particular, on the water samples with higher contents of detrital nitrogen and phosphorus. Our study result suggests that due to the existence of various forms of nitrogen and phosphorus in water samples and the different nutrient levels in lakes, the storage duration and the occurrence state of nitrogen and phosphorus should be considered when determining the nitrogen and phosphorus contents of water samples.