Recent advances in deep learning, especially the long short-term memory (LSTM) networks, provide some useful insights on how to tackle time series prediction problems, not to mention the development of a time series model itself for prediction. Runoff forecasting is a time series prediction problem with a series of past runoff data (water level and discharge series data) as inputs and a fixed-length series of future runoff as output. Most previous work paid attention to the sufficiency of input data and the structural complexity of deep learning, while less effort has been put into the consideration of data quantity or the processing of original input data—such as time series decomposition, which can better capture the trend of runoff—or unleashing the effective potential of deep learning. Mutual information and seasonal trend decomposition are two useful time series methods in handling data quantity analysis and original data processing. Based on a former study, we proposed a deep learning model combined with time series analysis methods for daily runoff prediction in the middle Yangtze River and analyzed its feasibility and usability with frequently used counterpart models. Furthermore, this research also explored the data quality that affect the performance of the deep learning model. With the application of the time series method, we can effectively get some information about the data quality and data amount that we adopted in the deep learning model. The comparison experiment resulted in two different sites, implying that the proposed model improved the precision of runoff prediction and is much easier and more effective for practical application. In short, time series analysis methods can exert great potential of deep learning in daily runoff prediction and may unleash great potential of artificial intelligence in hydrology research.