The data from 19 drill holes located in the hilly-plain region of the middle-lower reaches of the Changyuan River were systemically analyzed and, as a result, the predominant rock types of aquifers in the middle-lower reaches of the Changyuan River wetland were identified. Furthermore, based on the burial depth and development characteristics of aquifers and aquifuges, the authors divided the Quaternary aquifers in the study area into three aquifer sets, i.e., shallow, middle and deep aquifer sets. The features of spatial distribution of the aquifers in the study area were also summarized via correlation of cross sections and fence diagrams. In addition, the burial depths of groundwater tables were analyzed by using Kriging interpolation method. The results indicate that the predominant rock types of the aquifers are Quaternary sandy and gravel sediments. The profile of the shallow aquifer is like a wedged body in the downriver direction of the Changyuan River, but the thickness of the aquifer is not stable in the perpendicular direction of the river. This is in accordance with the sedimentary environment of the alluvial/fluvial fan. The results of interpolation analysis show that there are widely distributed precipitation funnels in the milled-lower reaches of the Changyuan River basin. Such a situation would impact the eco-hydrogeological process in the Changyuan River wetland park and the drainage basin. Finally, the authors discussed the recharge-discharge processes of the groundwater in the Changyuan River drainage basin and established a recharge-discharge model.