The seasonal variations in groundwater table would significantly change the dynamic responses of the ground and the screening performances of wave barriers. This paper develops a two-dimensional finite element model based on COMSOL to describe the propagation of waves in a layered ground with open trenches. This layered ground is modelled as a dry layer resting on a saturated half-space. The influence of the moving groundwater table on isolation efficiency of barriers is then investigated, considering the infiltrated water in trenches. The effects of soil hydraulic properties and geometrical parameters of the trench are also analyzed respectively. Results show that a low value of the permeability coefficient of saturated half-space may have a significantly detrimental effect on the screening performance due to the low frequency behaviors of the medium. Placing a trench in vibration-strengthening (weakening) zones results in a better (worse) isolation effect, and with a critical water table (Hw,c), increasing trench depth and width can hardly achieve a satisfactory screening efficiency (75% reduction) due to the occurrence of resonance in the dry layer. In addition, a multiple trench isolation system is simulated in the condition of high water levels and its shielding performance is compared to the single trench barrier. A triple trench barrier is found to be a preferred alternative because it can achieve a much better screening efficiency. Specially for Hw,c, a multiple trench barrier can effectively eliminate the adverse effect of the resonance and achieve more than 75% reduction of ground vibration.