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Massive amount of water level data has been collected by using Internet of Things (IoT) techniques in the Yangtze River and other rivers. In this paper, utilizing these data to construct deep neural network models for water level prediction is focused. To achieve higher accuracy, both the factors of time and locations of data collection sensors are considered to perform prediction. And the network structures of gated recurrent unit (GRU) and convolutional neural network (CNN) are combined to build a CNN-GRU model in which the GRU part learns the changing trend of water level, and the CNN part learns the spatial correlation among water level data observed from adjacent water stations. The CNN-GRU model that using data from multiple locations to predict the water level of the middle location has higher accuracy than the model only based on GRU and other state-of-the-art methods including autoregressive integrated moving average model (ARIMA), wavelet-based artificial neural network (WANN) and long-short term memory model (LSTM), because of its ability to decrease the affections of abnormal value and data randomness of a single water station to some extent. The results are verified on an experiment dataset that including 30-year observed data of water level at several collection stations in the Yangtze River. For forecasting the 8-o'clock water levels of future 5 days, accuracy of the CNN-GRU model is better than that of ARIMA, WANN and LSTM models with three evaluation factors including Nash-Sutcliffe efficiency coefficient (NSE), average relative error (MRE) and root mean square error (RMSE).