Deep learning has been used to improve intelligent transportation systems (ITS) by classifying ship targets in interior waterways. Researchers have created numerous classification methods, but they have low accuracy and misclassify other ship targets. As a result, more research into ship classification is required to avoid inland waterway collisions. We present a new convolutional neural network classification method for inland waterways that can classify the five major ship types: cargo, military, carrier, cruise, and tanker. This method can also be used for other ship classes. The proposed method consists of four phases for the boosting of classification accuracy for Intelligent Transport Systems (ITS) based on convolutional neural networks (CNNs); efficient augmentation method, the hyper-parameter optimization (HPO) technique for optimum CNN model parameter selection, transfer learning, and ensemble learning are suggested. All experiments used Kaggle’s public Game of Deep Learning Ship dataset. In addition, the proposed ship classification achieved 98.38% detection rates and 97.43% F1 scores. Our suggested classification technique was also evaluated on the MARVEL dataset. This dataset includes 10,000 image samples for each class and 26 types of ships for generalization. The suggested method also delivered an excellent performance compared to other algorithms, with performance metrics with an accuracy of 97.04%, a precision of 96.1%, a recall of 95.92%, a specificity of 96.55%, and a 96.31% F1 score.