Long-term climate change may strongly affect the aquatic environment in mid-latitude water resources. In particular, it can be demonstrated that temporal variations in surface water temperature in a reservoir have strong responses to air temperature. We adopted deep neural networks (DNNs) to understand the long-term relationships between air temperature and surface water temperature, because DNNs can easily deal with nonlinear data, including uncertainties, that are obtained in complicated climate and aquatic systems. In general, DNNs cannot appropriately predict unexperienced data (i.e., out-of-range training data), such as future water temperature. To improve this limitation, our idea is to introduce a transfer learning (TL) approach. The observed data were used to train a DNN-based model. Continuous data (i.e., air temperature) ranging over 150 years to pre-training to climate change, which were obtained from climate models and include a downscaling model, were used to predict past and future surface water temperatures in the reservoir. The results showed that the DNN-based model with the TL approach was able to approximately predict based on the difference between past and future air temperatures. The model suggested that the occurrences in the highest water temperature increased, and the occurrences in the lowest water temperature decreased in the future predictions.