Effective information regarding water yield response to climate change provides useful support for decision making in water resources management. By integrating a hydrology model into a systematic conservation model, we developed an approach for modeling impacts of climate change on the water cycles and constructing spatial priority conservation areas for water yield ecosystem services in Teshio watershed located in northernmost Japan. The climate changes were projected to have impacts in increasing surface runoff, lateral flow, groundwater discharge and water yield. Surface runoff especially decreased in April and May and increased in March and September with rising temperature. We then investigated the spatial hotspots of water yields in typical periods (February, April and October, annual average water yield) to determine spatially priority conservation areas for water resources in terms of their different protection targets. The results also indicated that the areas of spatial optimal protection for water yields across different periods dynamically changed from spatial and temporal standpoints. The optimal priority conservation areas were concentrated in the southwest, north and southeast of Teshio watershed through comprehensively taking into account water yields in typical periods. Our results indicated that combination of hydrology and systematic conservation models would improve sustainable management of water resources across the watershed.