Short-term traffic forecasting based on deep learning methods, especially recurrent neural networks (RNN), has received much attention in recent years. However, the potential of RNN-based models in traffic forecasting has not yet been fully exploited in terms of the predictive power of spatial–temporal data and the capability of handling missing data. In this paper, we focus on RNN-based models and attempt to reformulate the way to incorporate RNN and its variants into traffic prediction models. A stacked bidirectional and unidirectional LSTM network architecture (SBU-LSTM) is proposed to assist the design of neural network structures for traffic state forecasting. As a key component of the architecture, the bidirectional LSTM (BDLSM) is exploited to capture the forward and backward temporal dependencies in spatiotemporal data. To deal with missing values in spatial–temporal data, we also propose a data imputation mechanism in the LSTM structure (LSTM-I) by designing an imputation unit to infer missing values and assist traffic prediction. The bidirectional version of LSTM-I is incorporated in the SBU-LSTM architecture. Two real-world network-wide traffic state datasets are used to conduct experiments and published to facilitate further traffic prediction research. The prediction performance of multiple types of multi-layer LSTM or BDLSTM models is evaluated. Experimental results indicate that the proposed SBU-LSTM architecture, especially the two-layer BDLSTM network, can achieve superior performance for the network-wide traffic prediction in both accuracy and robustness. Further, comprehensive comparison results show that the proposed data imputation mechanism in the RNN-based models can achieve outstanding prediction performance when the model’s input data contains different patterns of missing values.