Recent global warming has been accompanied by high water temperatures (HWTs) in coastal areas of Korea, resulting in huge economic losses in the marine fishery industry due to disease outbreaks in aquaculture. To mitigate these losses, it is necessary to predict such outbreaks to prevent or respond to them as early as possible. In the present study, we propose an HWT prediction method that applies sea surface temperatures (SSTs) and deep-learning technology in a long short-term memory (LSTM) model based on a recurrent neural network (RNN). The LSTM model is used to predict time series data for the target areas, including the coastal area from Goheung to Yeosu, Jeollanam-do, Korea, which has experienced frequent HWT occurrences in recent years. To evaluate the performance of the SST prediction model, we compared and analyzed the results of an existing SST prediction model for the SST data, and additional external meteorological data. The proposed model outperformed the existing model in predicting SSTs and HWTs. Although the performance of the proposed model decreased as the prediction interval increased, it consistently showed better performance than the European Center for Medium-Range Weather Forecast (ECMWF) prediction model. Therefore, the method proposed in this study may be applied to prevent future damage to the aquaculture industry.