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Floods are of great concern as the global climate changes, and investigations of flood water infiltration and groundwater recharge are important for water resource management worldwide, especially under conditions of global climate changes. However, information on the relationship between the flood water and groundwater recharge is limited. The objective of this study was to determine the relationship between the flood water depth and the height of groundwater rise using lysimeters and numerical modeling in the floodplain of the Tarim River in northwestern China. The experimental results suggested that the rise in height of the groundwater table was closely related to the flood water ponding depth, and the groundwater depth decreased quickly after flooding due to the high infiltration rate of water originating at the Tarim River. The water table falling velocity was significantly less than the water table rising velocity. If the initial groundwater table was deeper, the variation in the water table rise depth was smaller and the water table falling velocity was slower. The numerical simulation results showed good agreement with the observed data, with a determination coefficient (R-2) of 0.87 and a root mean square error (RMSE) of 63.91 cm. A good relationship (R-2 = 0.789) between the initial groundwater table depth (H-0), initial soil water content (W-0), flood water depth (h), and height of the water table rise (H) was established. Considering that natural and artificial flood frequencies are related to flood time interval (dt), a relationship (R-2 = 0.892) was developed between them. These results can enhance the understanding of flood recharge characteristics in the floodplains of inland rivers.