Vessel traffic flow forecasting in port waterways is critical to improving safety and efficiency of port navigation. Aiming at the stage characteristics of vessel traffic in port waterways in time sequence, which leads to complexity of data in the prediction process and difficulty in adjusting the model parameters, a convolutional neural network (CNN) based on the optimization of the pelican algorithm (POA) and the combination of bi-directional gated recurrent units (BiGRUs) is proposed as a prediction model, and the POA algorithm is used to search for optimized hyper-parameters, and then the iterative optimization of the optimal parameter combinations is input into the best combination of iteratively found parameters, which is input into the CNN-BiGRU model structure for training and prediction. The results indicate that the POA algorithm has better global search capability and faster convergence than other optimization algorithms in the experiment. Meanwhile, the BiGRU model is introduced and compared with the CNN-BiGRU model prediction; the POA-CNN-BiGRU combined model has higher prediction accuracy and stability; the prediction effect is significantly improved; and it can provide more accurate prediction information and cycle characteristics, which can serve as a reference for the planning of ships’ routes in and out of ports and optimizing the management of ships’ organizations.