Earth System Models (ESMs) are progressively advancing towards the kilometer scale, involving changes such as mesh structure and input data resolution. Understanding the influence of these changes on water, energy, and carbon (WEC) cycles is crucial for modeling Earth system variability and change. This study conducts multiple experiments using the Energy Exascale Earth System Model Land and River Modeling (ELM-MOSART) over the Mid-Atlantic region for 1990–2014. These experiments consider factors related to mesh resolutions, land surface parameters, and atmospheric data that affect model simulations of water, energy, and carbon cycles. Specifically, we compare: (1) structured mesh (0.125 degrees) vs. unstructured variable resolution mesh (2–5 km); (2) land surface data sourced from different resolutions, 0.125 degrees vs. 1 km; and (3) three atmospheric forcings, GSWP3 (0.5 degrees) vs. NLDAS (0.125 degrees) vs. MSWX (0.1 degrees). Multiple benchmark datasets, including remote sensing data, gauge observations, and reanalysis datasets, were collected to evaluate model simulations over 2005–2014. The results show that high-resolution land surface data improves WEC simulations. Additionally, different atmospheric forcings also have a substantial impact on model simulations. These findings highlight the importance of considering mesh resolutions, land surface parameters, and atmospheric forcing in ESMs for accurate modeling of the water, energy, and carbon cycles.