<p>Over the recent decade, there has been a growing interest in analyzing the impacts of water bodies and greenery on microclimate and outdoor thermal comfort. However, there is a limited study regarding such an effect in a courtyard. This paper utilizes ENVI-met simulations to assess the cooling effect of water bodies and trees in a historical courtyard building in Shiraz, Iran. It aims to define the impact of water body size, layout, and tree arrangements. The novelty of this research lies in exploring the impact of altering established proportions of water and vegetation within the central courtyards. Four scenarios are designed to analyze their effect on courtyard microclimate and thermal conditions on the hottest and coldest days of the year. The results indicate that the microclimate and thermal comfort of the courtyard can be enhanced by increasing the size of the water body and implementing a proper layout. In summer, the air temperature can be reduced by 1.95&#xa0;°C, resulting in a 1.08&#xa0;°C decrease in the Universal Thermal Climate Index, due to the cooling effect of water bodies and trees. Additionally, the water body layout has a higher impact on thermal performance than the water surface area. With the same linear layout, tripling the water body size results in a 0.07–0.23&#xa0;°C decrease in air temperature and Universal Thermal Climate Index, respectively. The nonlinear layout aligned with prevailing winds (centralized or scattered) provides the greatest cooling efficiency, with a 1.17–1.08&#xa0;°C reduction in temperature and Universal Thermal Climate Index, respectively.</p>