In the smart mariculture, the timely and accurate predictions of water quality can help farmers take countermeasures before the ecological environment deteriorates seriously. However, the openness of the mariculture environment makes the variation of water quality nonlinear, dynamic and complex. Traditional methods face challenges in prediction accuracy and generalization performance. To address these problems, an accurate water quality prediction scheme is proposed for pH, water temperature and dissolved oxygen. First, we construct a new huge raw data set collected in time series consisting of 23,204 groups of data. Then, the water quality parameters are preprocessed for data cleaning successively through threshold processing, mean proximity method, wavelet filter, and improved smoothing method. Next, the correlation between the water quality to be predicted and other dynamics parameters is revealed by the Pearson correlation coefficient method. Meanwhile, the data for training is weighted by the discovered correlation coefficients. Finally, by adding a backward SRU node to the training sequence, which can be integrated into the future context information, the deep Bi-S-SRU (Bi-directional Stacked Simple Recurrent Unit) learning network is proposed. After training, the prediction model can be obtained. The experimental results demonstrate that our proposed prediction method achieve higher prediction accuracy than the method based on RNN (Recurrent Neural Network) or LSTM (Long Short-Term Memory) with similar or less time computing complexity. In our experiments, the proposed method takes 12.5ms to predict data on average, and the prediction accuracy can reach 94.42% in the next 3∼8 days. INDEX TERMS Smart mariculture, precision agriculture, water quality prediction, SRU, deep learning.