Due to the high heterogeneity and complexity of water flow movement for multiple karst water-bearing mediums, the evaluation, effective development, and utilization of karst water resources are significantly limited. Matrix flow is usually laminar, whereas conduit flow is usually turbulent. The driving mechanisms of water exchange that occur between the karst conduit and its adjacent matrix are not well understood. This paper investigates the hydrodynamic characteristics and the mechanism of flow exchange in dual water-bearing mediums (conduit and matrix) of karst aquifers through laboratory experimentation and numerical simulation. A karst aquifer consisting of a matrix network and a conduit was proposed, and the relationship between the water exchange flux and hydraulic head differences generated from the laboratory experiments was analyzed. Two modes of experimental tests were performed with different fixed water level boundaries in the laboratory karst aquifer. The results indicate that the water exchange capacity was proportional to the square root of hydraulic head differences. The linear exchange term in the conduit flow process (CFP) source program was modified according to experimental results. The modified CFP and the original CFP model experimental data results were compared, and it was found that the modified CFP model had better fitting effects. These results showed that the water exchange mechanism between conduit and matrix is very important for solid-liquid interface reaction, water resource evaluation, and understanding of karst hydrodynamic behavior.