Based on the first linearized Boussinesq equation, the analytical solution of the transient groundwater model, which is used for describing phreatic flow in a semi-infinite aquifer bounded by a linear stream and subjected to
time-dependent vertical seepage, is derived out by Laplace transform and the convolution integral. According to the mathematical characteristics of the solution, different methods for estimating aquifer parameters are constructed to satisfy different hydrological conditions. Then, the equation for estimating water exchange between stream and aquifer is proposed, and a recursion equation or estimating the intensity of phreatic evaporation is also proposed. A phreatic aquifer stream system located in Huaibei Plain, Anhui Province, China, is taken as an example to demonstrate the estimation process of the methods stated herein.