Machine learning has been used to mine the massive data collected by automatic environmental monitoring systems and predict the changes in the environmental factors in lakes. However, further study is needed to assess the feasibility of the development of a universal machine-learning-based turbidity model for a large shallow lake with considerable spatial heterogeneity in environmental factors. In this study, we collected and examined sediment and water quality data from Lake Taihu, China. Three monitoring stations were established in three lake zones to obtain continuous time series data of the water quality and meteorological variables. We used these data to develop three turbidity models based on long short-term memory (LSTM). The three zones differed in terms of environmental factors related to turbidity: in West Taihu, the Lake Center, and the mouth of Gonghu Bay, the critical shear stress of bed sediments was 0.029, 0.055, and 0.032 N m−2, and the chlorophyll-a concentration was 23.27, 14.62, 30.80 μg L−1, respectively. The LSTM-based turbidity model developed for any zone could predict the turbidity in the other two zones. For the model developed for West Taihu, its performance to predict the turbidity in the local zone (i.e., West Taihu) was inferior to that for the other zones; the reverse applied to the models developed for the Lake Center and Gonghu Bay. This can be attributed to the complex hydrodynamics in West Taihu, which weakens the learning of LSTM from the time series data. This study explores the feasibility of the development of a universal LSTM-based turbidity model for Lake Taihu and promotes the application of machine learning algorithms to large shallow lakes.