In this study, the amount of harmful fungi and bacteria contained in the drainage and culture medium from the paprika hydroponic facility is identified. In addition, by proposing the necessity of effective purification of discharged drainage, this study attempted to confirm the possibility of drainage reuse. Finally, this study provides basic data on the basis for calculating the need for purification facilities in the future, as well as improvements in horticulture facility for sustainable agriculture. As a result of the analysis, a total of 12 types of fungi were detected in paprika medium and 10 types of fungi were detected in the drainage, and their densities were 130 and 68, respectively. Among the fungi detected in the media and drainage of the paprika hydroponic facility, the fungi with the highest detection frequency are Fusarium, Phytophthora, and Pythium. In the case of bacteria, a total of 2 types of bacteria were detected in the paprika facilities, and the density was 28 and 23, respectively. Therefore, in order to reuse the drainage and settle the circulating hydroponic cultivation system, a water treatment process capable of appropriate treatment is required.