The stable operation of the Francis turbine unit (FTU) determines the safety of the hydropower plant and the energy grid. The traditional FTU performance evaluation methods with a fixed threshold cannot avoid the influence of variable operating conditions. Meanwhile, anomaly samples and missing values in the low-quality on-site data distort the monitoring signals, which greatly affects the evaluation and prediction accuracy of the FTU. Therefore, an approach to the performance evaluation and prediction of the FTU considering low-quality data and variable operating conditions is proposed in this study. First, taking the variable operating conditions into consideration, a FTU on-site data-cleaning method based on DBSCAN is constructed to adaptively identify the anomaly samples. Second, the gate recurrent unit with decay mechanism (GRUD) and the Wasserstein generative adversarial network (WGAN) are combined to propose the GRUD–WGAN model for missing data imputation. Third, to reduce the impact of data randomness, the healthy-state probability model of the FTU is established based on the GPR. Fourth, the prediction model based on the temporal pattern attention–long short-term memory (TPA–LSTM) is constructed for accurate degradation trend forecasting. Ultimately, validity experiments were conducted with the on-site data set of a large FTU in production. The comparison experiments indicate that the proposed GRUD–WGAN has the highest accuracy at each data missing rate. In addition, since the cleaning and imputation improve the data quality, the TPA–LSTM-based performance indicator prediction model has great accuracy and generalization performance.