An important problem associated with the aerial mapping of the seabed is the precise classification of point clouds characterizing the water surface, bottom, and bottom objects. This study aimed to improve the accuracy of classification by addressing the asymmetric amount of data representing these three groups. A total of 53 Synthetic Minority Oversampling Technique (SMOTE) algorithms were adjusted and evaluated to balance the amount of data. The prepared data set was used to train the Multi-Layer Perceptron (MLP) neural network used for classifying the point cloud. Data balancing contributed to significantly increasing the accuracy of classification. The best overall classification accuracy achieved varied from 95.8% to 97.0%, depending on the oversampling algorithm used, and was significantly better than the classification accuracy obtained for unbalanced data and data with downsampling (89.6% and 93.5%, respectively). Some of the algorithms allow for 10% increased detection of points on the objects compared to unbalanced data or data with simple downsampling. The results suggest that the use of selected oversampling algorithms can aid in improving the point cloud classification and making the airborne laser bathymetry technique more appropriate for seabed mapping.