A pump-type eDNA filtering system that can control voltage and hydraulic pressure respectively has been developed, and applied a filter case that can filter out without damaging the filter. The filtering performance of the developed system was evaluated by comparing the eDNA concentration with the conventional vacuum-pressured filtering method at the catchment conduit intake reservoir. The developed system was divided into a voltage control (manual pump system) method and a pressure control (automatic pump system) method, and the pressure was measured during filtering and the pressure change of each system was compared. The voltage control method started with 65 [KPa] at the beginning of the filtering, and as the filtering time elapsed, the amount of filtrate accumulated in the filter increased, so the pressure gradually increased. As a result of controlling the pressure control method to maintain a constant pressure according to the designed algorithm, there was a difference in the width of the hydraulic pressure fluctuation during the filtering process according to the feedback time of the hydraulic pressure sensor, and it was confirmed that the pressure was converged to the target pressure. The filtering performance of the developed system was confirmed by measuring the eDNA concentration and comparing the voltage control method and the hydraulic control method with the control group. The voltage control method obtained similar results to the control group, but the hydraulic control method showed lower results than the control group. It is considered that the low eDNA concentration in the hydraulic control method is due to the large pressure deviation during filtering and maintaining a constant pressure during the filtering process. Therefore, rather than maintaining a constant pressure during filtering, it was confirmed that a voltage control method in which the pressure is gradually increased as the filtrate increases with the lapse of filtering time is suitable for collecting eDNA. As a result of comparing the average concentration of eDNA in lentic zone and lotic zone as a control group, it was found to be 96.2 [ng μL-1] and 88.4 [ng μL-1l], respectively. The result of comparing the average concentration of eDNA by the pump method was also high in the lentic zone sample as 90.7 [ng μL-1] and 74.8 [ng μL-1] in the lentic zone and the lotic zone, respectively. The high eDNA concentration in the lentic zone is thought to be due to the influence of microorganisms including the remaining eDNA.