Following the alarming reports of microplastic pollution in the marine environment, increased attention has been given to microplastics in other environmental media. Despite the attention, there is limited research available on the depth-distribution of microplastics in freshwater. Specifcally, in the case of water sources used for drinking or tap, the height of intake facilities varies, and it is highly likely that there is a correlation between the vertical distribution of microplastics and these water intake structures. Further, because the size of microplastics varies widely in the environment, the commonly used sampling devices are not suitable for selectively extracting microplastics without causing cross-contamination. Thus, we developed a suitable device for microplastics of size 5–20 µm and studied microplastic distribution in freshwater at various depths by considering various types of microplastics and aqueous systems. Lake and river, two major water sources, were selected for the study of microplastics distribution in water system. The microplastic distribution characteristics in both water systems showed that polypropylene and polyethylene were the most abundant across all depths because of their production volume. Plastic types with higher density were found only at the lower layers, and polystyrene was found in the upper layers because of the environmental efects on its buoyancy caused pore diameter and surface area. The lake and river had higher microplastic distribution in the lower layer and upper layer, respectively. This was because the fow rate in river was higher than that of lake. The higher fow rate reduced the settling velocity in river. Thus, hydrodynamic stability infuences the vertical distribution and concentrations of microplastics in the water systems. These results are expected to be used for understanding the behavioral characteristics of microplastics in water systems and to manage water sources.