Globally, the deterioration of aquatic ecosystems has attracted wide concentrations of scholars and governments, and how to wisely remediate the damaged ecosystem is a hot issue. Determination of prior areas is critical for ecosystem remediation. However, there are very few systematically feasible methods available for comprehensively addressing the issue, and consequently, the benefits of water ecosystem remediation projects are reduced. Therefore, this paper proposes a framework for determining priority areas based on phytoplankton response to environmental factors. Phytoplankton constitute the main component of global aquatic biomes and water blooms. The effects of water ecosystem remediation projects are highly related to phytoplankton. First, we identified the dominant species of phytoplankton using a dominance accumulation model. Then, we determined the main environmental factors of phytoplankton using detrended correspondence analysis and canonical correspondence analysis. Afterwards, we calculated the adaptability of a single species to all principal environmental factors and the responsiveness of all dominant species to a single environmental factor using methods of integrated habitat suitability index and multispecies‐based habitat suitability index. On the basis of these results, we finally developed a new model of the suitability of aquatic biomes to habitat factors (IHSIA) whereby to determine the priority areas and the principal environmental factors by time–space coupling analysis. We applied the method to Jinan, a pilot city for the construction of a civilized ecological city in China. The results indicated that waters in urban areas are priority areas for remediation; principal environmental factors in both the whole study area and the priority areas for phytoplankton are NH3‐N, water temperature, total phosphorus, and dissolved oxygen where the NH3‐N is the most urgent environmental factor to be remediated in the study area. Reducing the concentration of NH3‐N can facilitate phytoplankton biome remediation. We found that dominant phytoplankton species can reflect the actual status of phytoplankton populations and can provide important reference data for global aquatic life research; space–time scale is an important factor in selecting principal environmental factors; limiting environmental factors that are poorly adaptable to dominant species could help provide a new path for water bloom prevention; the newly proposed model IHSIA can make the ecological environment remediation more objective. These results can help water managers reduce the scale of phytoplankton biomes by adjusting the environmental factors. The presented framework can provide new ways for water bloom prevention and can serve as the theoretical and scientific basis for the high success rate of water ecosystem restoration projects across the world.
