Carbon dioxide (CO2) sequestration in depleted shale reservoirs is a promising approach for reducing greenhouse gas emissions while enhancing the recovery of adsorbed methane (CH4). However, the injection of CO2 into shale formations containing water can alter the pH conditions within the nanopores quartz minerals, influencing the adsorption behavior of CO2 and CH4. This study employed grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations to investigate the single-component adsorption of CO2 and CH4, as well as their competitive co-adsorption, in quartz nanopores under varying pH conditions. Three quartz models with deprotonation degrees of 0% (pH 2–4), 9% (pH 5–7), and 18% (pH 7–9) were considered, representing a range of reservoir pH environments. In the absence of water, increasing the pH enhanced the affinity between CO2 and the quartz surface, resulting in higher adsorption densities and over 50% of the CO2 existing in an adsorbed state at high pH. However, the presence of pre-adsorbed water significantly altered the adsorption characteristics. At low pH (0% deprotonation), water covered less of the quartz surface, leaving more available adsorption sites that favored CO2 sequestration, with over 40% existing in an adsorbed state. In competitive co-adsorption without water, higher pH promoted greater displacement of adsorbed CH4 by CO2. Conversely, with pre-adsorbed water, a lower pH was more beneficial for displacing CH4. These findings elucidate how pH-induced changes in quartz surface chemistry influence the adsorption dynamics of CO2 and CH4, providing molecular-level insights to guide CO2 sequestration strategies and improved recovery of adsorbed CH4 from depleted shale reservoirs under varying formation water conditions.