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Abstract The U.S. water supply and carbon sequestration are increasingly threatened by future climate change and air pollution. This study investigates the ecohydrological responses to the individual and combined impacts of climate change and anthropogenic emission (referring only to air pollutants, excluding greenhouse gases) changes at two spatial scales by coupling a regional online‐coupled meteorology and chemistry model (WRF‐Chem) and a water balance model (WaSSI). Combined effects of climate change and anthropogenic emission changes in 2046–2055 relative to 2001–2010 over the US enhance hydrological cycle and carbon sequestration. However, a drying trend occurs in the central and part of the western U.S. Climate change is projected to dominate the ecohydrological changes in most regions. Anthropogenic emission changes under 2001–2010 climate conditions cools down inland water resource regions with 0.01–0.15°C, moisturizes the east and dry the west U.S. More stringent anthropogenic emission control enhances precipitation and ecosystem production in the east and west but has an opposite trend in the central U.S. The ecohydrological modeling in California and North Carolina based on 4‐km resolution meteorological data in 2050 and 2005 shows varying changes in magnitudes and spatial patterns compared to results based on 36‐km resolution meteorological data. Projected changes in air pollutant emissions may accelerate climatic warming in coastal areas and the state of New Mexico and decrease precipitation, runoff, and carbon sequestration in part of the western U.S. Strategies to address future possible problems such as heatwaves, water stress, and ecosystem productivity should consider the varying interplay between air quality control and climate change at different spatial scales.