Nutrient releasing at the sediment-water interface (SWI) is the focus of environmental behavior research in lakes, but there is a lack of lateral quantitative comparison in the methods used to estimate lake fluxes. In this paper, Lake Mochou in Nanjing was taken as the research object, and four common lake flux estimation methods, such as static release method, mechanical agitation method, flow cultivation method and pore water concentration diffusion model method, were used to conduct comparative experiments on nitrogen and phosphorus release in winter, spring and summer. The results showed that the non-diffusion model (static release, mechanical agitation and flow cultivation) had negative flux in the winter, and the estimated flux was positive in the summer with the increase in temperature, and there was no significant difference in the flux values between the three methods. The results of the pore water diffusion model method showed no negative values in the three-season tests, which were significantly different from those of the non-diffusion model groups with about one order of magnitude lower. There were significant differences in dissolved oxygen and pH among different methods, and the flow cultivation method was the most stable. The flux results of the four methods were significantly correlated with each other in different seasons. As the apparent flux value, the estimation results of the non-diffusion model method were suitable for calculating the total nutrient release of lake sediments. The static release method showed poor stability, and the relative standard deviation of the parallel group was up to 70%. The flow cultivation method had the best stability, and the relative standard deviation of the parallel group was only 21%. As the theoretical release value, the estimated result of the diffusion model is lower than the actual release flux of shallow lake flux, which is suitable for exploring the dynamic release process of sediment interstitial water in deep-water lakes and helpful for analyzing the properties of lake sediments. Different cultivation methods have their own emphases. According to different lake conditions and experimental needs, appropriate methods should be selected for flux estimation.