In the practical production environment, the complexity and variability of hydroelectric units often result in a need for more fault data, leading to inadequate accuracy in fault identification for data-driven intelligent diagnostic models. To address this issue, this paper introduces a novel fault diagnosis method tailored for unbalanced small-sample states in hydroelectric units based on the Wasserstein generative adversarial network (W-GAN). Firstly, the fast Fourier transform is used to convert the signal from the time domain to the frequency domain to obtain the spectral data, and the W-GAN is trained to generate false spectral data with the same probability distribution as the real fault data, which are combined with the actual data and inputted into the 1D-CNN for feature extraction and fault diagnosis. In order to assess the effectiveness of the proposed model, a case study was conducted using actual data from a domestic hydropower plant, and the experimental results show that the sample features can be effectively enriched via data enhancement performed on small-sample data to improve the accuracy of fault diagnosis, which verifies the effectiveness of the method proposed in this paper.