Marine Stratocumulus clouds are prevalent over the eastern boundary of the subtropical oceans (e.g. northeast and southeast Pacific). Due to their shortwave properties, these low clouds significantly impact the regional and global climate. However marine stratocumulus clouds are subject to modeling approximations as well as, numerous uncertainties on the factors contributing to their radiative properties, variability and possible future changes. In this dissertation, we present three regional modeling studies that intend to provide some more understanding to these issues. We first analyze the sensitivity of marine stratocumulus to parameterizations in the Weather Research and Forecasting (WRF) model. We use the southeast Pacific as a testbed region and compare the simulated surface energy fluxes to those measured during VOCALS-REx. Our results show that errors in shortwave fluxes are traceable to errors in liquid water path (LWP). Two mechanisms controlling the LWP in our simulations are diagnosed. The first mechanism involves boundary layer and shallow cumulus schemes, which control moisture available for cloud by regulating boundary layer height. The second mechanism involves microphysics schemes, which control LWP through the production of drizzle. This study demonstrates that when parameterizations are appropriately chosen, the stratocumulus deck and the related surface energy fluxes are reasonably well represented in WRF. In s second study, we take advantage of these advancements to evaluate the importance of aerosol indirect effects on clouds shortwave properties in the northeast Pacific. Satellite retrievals (e.g. MODIS) show that the cloud droplet number concentration is generally high along the U.S. west coast (~300cm-3), while it drops to smaller values further offshore (~50cm-3). Our results highlight the importance of representing accurately this aerosol spatial variability and the associated indirect effects on LWP for realistic shortwave fluxes simulations in the northeast Pacific. Finally, we analyze the marine stratocumulus variability and their possible anthropogenic changes using a suite of dynamically downscaled experiments in the California region. In particular, we develop a methodology that enables a clear identification of the factors contributing to low cloud cover anthropogenic changes. Our results show a systematic reduction in low cloud cover, which is mostly imputable to a reduction of the coupling between boundary layer top and surface. Our analysis suggests that the enhanced decoupling conditions might be at least partially driven by the drying of the free troposphere in comparison to the boundary layer in future climate.