Harmful organisms in the marine environment can have devastating impacts on fisheries, and marine ecosystems, and even cause harm to humans. Therefore, early detection and effective management are crucial. In recent years, eDNA monitoring has become an important tool for detecting aquatic organisms. Species-specific eDNA monitoring offers advantages over NGS methods, such as metabarcoding, as it is more cost-effective. This economic advantage has led to the widespread use of species-specific eDNA monitoring, particularly for detecting harmful organisms. In this study, eDNA monitoring was conducted for HABs, Cnidaria, and Echinodermata, which are designated as representative harmful organisms by the Republic of Korea. The monitoring was conducted in Masan Bay, South Korea, which is known to be heavily polluted in the past. The selective detection of harmful organisms in seawater using eDNA demonstrated the superiority of this technology over conventional morphological methods in terms of speed, accuracy, non-invasiveness, and non-destructiveness. Comparative analysis with microscopic examination of HABs further supported these advantages. The specific primers and monitoring methods presented in this study enable specific-species and selective detection, and they offer greater reproducibility compared to conventional morphological monitoring methods. Consequently, for the first time in South Korea, all 12 species of environmental factors and harmful organisms in Masan Bay were detected using eDNA, a method that relies less on specialized knowledge and is more cost-effective compared to existing methods. These findings hold great promise for environmental conservation, fisheries development, and the effective detection and management of harmful organisms in marine environments.