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As a component of arid ecosystems, groundwater plays an important role in plant growth; therefore, it is essential to use deterministic models to reconstruct the process of groundwater level change. Typically, the linearized solution of the one-dimensional (1-D) Boussinesq equation yields acceptable performance in simulating transient conditions over short recharge periods in ephemeral stream systems, but the ability of this solution to simulate multiyear changes in groundwater levels is limited. In this study, an improved groundwater hydraulics (GH-D2) model is built based on the groundwater hydraulics (GH) solution of the 1-D Boussinesq equation to simulate multiyear changes in the groundwater level in ephemeral stream systems. The model is validated in the lower reaches of the Tarim River to simulate groundwater level fluctuations within the scope of influence of the river (300, 500, 750, 1050 m) over a 16-year period (2000 to 2015). To evaluate the performance of the models, the bias, mean absolute error, root mean squared error, Nash-Sutcliffe efficiency (NSE), and coefficient of determination (R-2) are calculated. The results show that the improved GH-D2 model, which considers ephemeral streamflow, unsteady flow theory and the delayed response effect of groundwater level changes, performs well in simulating multiyear changes in the groundwater level in the ephemeral stream system. The observed and simulated values of the groundwater level at different river distances are consistent, and the model provides a new basis for multiyear simulations of groundwater level fluctuations in ephemeral stream systems.