Changes in soil parameters such as saturated unit weight (body force), hydraulic conductivity, and elastic modulus must be considered for simulating aquitard consolidation. In addition to changes in soil parameters, grid intervals change the subsequent soil deformation in such simulations. This study incorporated and examined the effects of both the grid deformation and soil parameter variation on the numerical simulation of aquitard consolidation caused by hydraulic head decline in a multilayered aquifer system. According to the nondimensional analysis, the deformation number can be regarded as a dimensionless parameter for assessing whether the grid deformation and soil parameter variation affect this simulation. The results revealed that when the deformation number exceeds 0.01 (i.e., when the aquitard is thick or soft), both the grid deformation and soil parameter variation must be simultaneously considered to increase accuracy. Aquitard consolidation was always overestimated when only the soil parameter variation was considered. However, when only the grid deformation was considered, the aquitard consolidation was either overestimated or underestimated depending on whether the influence of the change in the body force was more substantial than that of the elastic modulus.