Identifying priority zones for river restoration is important for biodiversity conservation and catchment management. However, limited data due to the difficulty of field collection has led to research to better understand the ecological status within a catchment and develop a targeted planning strategy for river restoration. To address this need, coupling hydrological and machine learning models were constructed to identify priority zones for river restoration based on a dataset of aquatic organisms (i.e., algae, macroinvertebrates, and fish) and physicochemical indicators that were collected from 130 sites in September 2014 in the Taizi River, northern China. A process-based model soil and water assessment tool (SWAT) was developed to model the temporal-spatial variations in environmental indicators. A support vector machine (SVM) model was applied to explore the relationships between aquatic organisms and environmental indicators. Biological indices among different hydrological periods were simulated by coupling SWAT and SVM models. Results indicated that aquatic biological indices and physicochemical indicators exhibited apparent temporal and spatial patterns, and those patterns were more evident in the upper reaches compared to the lower reaches. The ecological status of the Taizi River was better in the flood season than that in the dry season. Priority zones were identified for different hydrological seasons by setting the target values for ecological restoration based on biota organisms, and the results suggest that hydrological conditions significantly influenced restoration prioritization over other environmental parameters. Our approach could be applied in other seasonal river ecosystems to provide important preferences for river restoration.