The objective of this study was to evaluate fish habitat suitability by simulating hydrodynamic and water quality factors using integration model of SWAT and HEC-RAS models considering time-series analysis. The 2.9 km reach of the Bokha stream was selected for the habitat evaluation of Zacco platypus, a dominant fish species of the stream reach. Streamflow and water quality at stream inlet were simulated with the SWAT model and subsequent cross-sectional stream velocity and water depth along with water temperature and dissolved oxygen (DO) were estimated using the HEC-RAS. The linked model was calibrated and validated for the 10 years period from 2013 to 2022. The aquatic habitat was assessed using the weighted usable area (WUA) and time-series analysis was conducted considering the continuity of stream habitat. Overall, SWAT and HEC-RAS simulation accuracy were evaluated as satisfactory or higher in all habitat influence indicators. High water temperature appeared to be the most influential habitat indicator of which impact was particularly pronounced in shallow streamflow areas during hot summer seasons. The time-series analysis identified a 28% threshold of WUA/WUAmax, equivalent to a streamflow of 0.48 m³/s, as the minimum ecological streamflow to mitigate the impact of water temperature rise. The proposed method by linking watershed-stream models could serve as a useful tool for ecological stream management.