This paper proposes a new fault diagnosis method for centrifugal pumps by combining signal processing with deep learning techniques. Centrifugal pumps facilitate fluid transport through the energy generated by the impeller. Throughout the operation, variations in the fluid pressure at the pump’s inlet may impact the generalization of traditional machine learning models trained on raw statistical features. To address this concern, first, vibration signals are collected from centrifugal pumps, followed by the application of a lowpass filter to isolate frequencies indicative of faults. These signals are then subjected to a continuous wavelet transform and Stockwell transform, generating two distinct time–frequency scalograms. The Sobel filter is employed to further highlight essential features within these scalograms. For feature extraction, this approach employs two parallel convolutional autoencoders, each tailored for a specific scalogram type. Subsequently, extracted features are merged into a unified feature pool, which forms the basis for training a two-layer artificial neural network, with the aim of achieving accurate fault classification. The proposed method is validated using three distinct datasets obtained from the centrifugal pump under varying inlet fluid pressures. The results demonstrate classification accuracies of 100%, 99.2%, and 98.8% for each dataset, surpassing the accuracies achieved by the reference comparison methods.