Land subsidence is a serious problem in Taiwan’s Yunlin area due to groundwater overpumping. There are safety risks in the high-speed railway structures in the areas of Siluo, Huwei, Tuku, and Yuanchang towns that run from north to south in the Yunlin area. Therefore, it is important to increase the groundwater recharge and to remedy the land subsidence in this area. The purpose of this study is to use the stream-flow estimation model (SF) and the groundwater flow numerical software MODFLOW (MF) to estimate the stream infiltration with consideration to the variation of the river water level in the Hsinhuwei River. The Ferris analytical model (FA) and MF are used to estimate the increased stream infiltration after the water level of the river rises. The hydraulic parameters required for each model are obtained from field observations and laboratory experiments. The results indicate that the assessment of the stream infiltration obtained through the SF and MF models are 264.2 × 104 and 170.9 × 104 m3/year, respectively. When the river water level increases by about 2.5 m, the annual stream infiltration obtained through the FA and MF models significantly increases by 31.6 × 104 and 26.4 × 104 m3/year, respectively. Taken together, the stream storages estimated using these two models indicate that an increasing efficiency of groundwater recharge is within the range of 10.0–18.5%.