Dredging is a basic construction for waterway improvement, harbor basin maintenance, land reclamation, environmental protection dredging, and deep-sea mining. The dredging process of cutter suction dredgers is so complex that the operational data show strong characteristics of dynamic, nonlinearity, and time delay, which make it difficult to predict the productivity accurately via basic principles models. In this paper, we propose a novel integrating PCA-LSTM model to improve the productivity prediction of cutter suction dredger. Firstly, multiple variables are reduced in dimension and selected by PCA method based on the working mechanism of cutter suction dredger. Then the productivity is predicted via mud concentration in long short-term memory network with relevant operational time-series data. Finally, the proposed method is successfully applied to an actual case study in China. Also, it performs well in the cross-validation and comparative study for several important characteristics: (i) it involves the operational parameters based on the mechanism analysis; and (ii) it is a deep-learning-based approach that can deal with operation series data with a special memory mechanism. This study provides a heuristic idea for integrating the data-driven method and supervision of human knowledge for application in practical engineering.