Water environment protection is of great significance for both economic development and improvement of people's livelihood, where modeling of water environment evolution is indispensable in water quality analysis. However, many water quality indexes related to water quality model cannot be measured online, and some model parameters always vary among different water areas. Thus, this paper proposes a water quality soft-sensing method based on the water quality mechanism model to simulate evolution of water quality indexes online, where unscented Kalman filter is utilized to estimate model parameters. Furthermore, a modified fuzzy comprehensive evaluation method is presented to evaluate the level of water eutrophication condition. Finally, the water quality data collected from Taihu Lake and Beihai Lake are used to validate the effectiveness and generality of the proposed method. The results show that the proposed soft-sensing method is able to describe the variation of related water quality indexes, with better accuracy compared to nonlinear least squares based method and traditional trial-and-error based method. On this basis, the water eutrophication condition can be also accurately evaluated.