Accurately predicting hydrological runoff is crucial for water resource allocation and power station scheduling. However, there is no perfect model that can accurately predict future runoff. In this paper, a daily runoff prediction method with a seasonal decomposition-based-deep gated-recurrent-unit (GRU) method (SD-GRU) is proposed. The raw data is preprocessed and then decomposed into trend, seasonal, and residual components using the seasonal decomposition algorithm. The deep GRU model is then used to predict each subcomponent, which is then integrated into the final prediction results. In particular, the hyperparameter optimization algorithm of tree-structured parzen estimators (TPE) is used to optimize the model. Moreover, this paper introduces the single machine learning model (including multiple linear regression (MLR), back propagation (BP), long short-term memory neural network (LSTM) and gate recurrent unit (GRU)) and a combination model (including seasonal decomposition–back propagation (SD-BP), seasonal decomposition–multiple linear regression (SD-MLR), along with seasonal decomposition–long-and-short-term-memory neural network (SD-LSTM), which are used as comparison models to verify the excellent prediction performance of the proposed model. Finally, a case study of the Qingjiang Shuibuya test set, which considers the period 1 January 2019 to 31 December 2019, is conducted. Case studies of the Qingjiang River show the proposed model outperformed the other models in prediction performance. The model achieved a mean absolute error (MAE) index of 38.5, a Nash-Sutcliffe efficiency (NSE) index of 0.93, and a coefficient of determination (R2) index of 0.7. In addition, compared to the comparison model, the NSE index of the proposed model increased by 19.2%, 19.2%, 16.3%, 16.3%, 2.2%, 2.2%, and 1.1%, when compared to BP, MLR, LSTM, GRU, SD-BP, SD-MLR, SD-LSTM, and SD-GRU, respectively. This research can provide an essential reference for the study of daily runoff prediction models.