Water is the source of life and the fundamental element of ecology, and climate is inseparable from water. To evaluate the influence of water-adaptive space in a traditional Weizi (polder village) settlement on its microclimate, the authors analyzed the morphological characteristics of such a polder village and applied the ENVI-met model to simulate the impact of water bodies and village morphological elements on human thermal comfort. This paper demonstrates the positive impact of water bodies on improving the thermal environment of a village and regulating its microclimate by quantifying the impact of morphological elements of the settlement on microclimate. The results indicate that: 1) The simulation model fits the actual measurements well, and the simulation accurately reflects experimental results; 2) In summer, the cooling effect of water bodies is better in the afternoon than in the morning, especially from 12:00 to 15:00. The cooling effect is significantly correlated with the distance to water bodies, i.e., the closer, the better; 3) Building density and man-made underlying surface are negatively correlated with temperature, humidity, and Physiological Equivalent Temperature value, while greening rate and water body rate are positively correlated with microclimate. Overall, water bodies can improve outdoor comfort in summer and thus should be protected and developed in rural planning and design. Villages can be built around water bodies for a maximized cooling effect, and microclimate comfort can be effectively improved by increasing green plants near the village center, and reducing man-made underlying surface and building density. The results of this study will guide the improvement of the habitat environment in the process of rural revitalization, as well as the protection and re-development of traditional villages.