The Model of Emissions of Gases and Aerosol from Nature (MEGAN) is widely used for estimating BVOC (Biogenic volatile organic compounds) in global and regional models. Nevertheless, MEGAN lacks correct representation of canopy resistance and soil moisture processes. These deficiencies are addressed by coupling MEGAN with a photosynthesis-based Gas-Exchange Model (GEM) implemented at each level to resolve stomatal resistance in a multi-layer vegetation canopy model within Noah land-surface/hydrology model framework. One main goal of this study is to investigate the degree to which seasonally varying soil moisture, soil temperature, and canopy resistance affect isoprene emission rate. A two-year numerical experiment is conducted by using the HRLDAS (High Resolution Land Data Assimilation System), in which a number of high-resolution atmospheric observations and land/vegetation data are used to drive the coupled Noah-GEM-MEGAN in uncoupled mode with 3-km grid-spacing over the Rocky Mountain regions of Colorado and adjoining states. We will discuss how different hydrological processes (e.g., runoff, snow, evaporation) affect long-term evolution of soil moisture and temperature and influence the warm-season isoprene emission rate, because soil moisture directly modify both the canopy resistance and BVOC emission. Also will be discussed is the relationship between spatial distribution of soil moisture, surface evaporation, surface temperature, and isoprene emission.