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Vacuum is an important parameter in cutter suction dredging operations because the equipment is underwater and can easily fail. It is necessary to analyze other parameters related to the vacuum to make real-time predictions about it, which can improve the construction efficiency of the dredger under abnormal working conditions. In this paper, a data-driven method for predicting the vacuum of the underwater pump of the cutter suction dredger (CSD) is proposed with the help of big data, machine learning, data mining, and other technologies, and based on the historical data of “Hua An Long” CSD. The method eliminates anomalous data, standardizes the data set, and then relies on theory and engineering experience to achieve feature extraction using the Spearman correlation coefficient. Then, six machine learning methods were employed in this study to train and predict the data set, namely, lasso regression (lasso), elastic network (Enet), gradient boosting decision tree (including traditional GBDT, extreme gradient boosting (XGBoost), light gradient boosting machine (LightGBM)), and stacking. The comparison of the indicators obtained through multiple rounds of feature number iteration shows that the LightGBM model has high prediction accuracy, a good running time, and a generalization ability. Therefore, the methodological framework proposed in this paper can help to improve the efficiency of underwater pumps and issue timely warnings in abnormal working conditions. Full article