Industrial effluent containing heavy metals discharged into streams may pose high toxicity risks to aquatic organisms and to human health. Therefore, it is important to understand how to change the amount of effluent with heavy metals discharged from industries into open aquatic ecosystems both for effective management of heavy metals and to foster sustainable ecosystems. This study was conducted to characterize the release of heavy metals from industries based on the Pollutant Release and Transfer Registers database in Korea from 1999 to 2010. From the database, we selected nine heavy metals (Pb, Cd, Mn, Sb, Cu, Zn, Cr, Sn, and Ni) and compared the differences in their effluent for different types of industries. The heavy metal effluents released into freshwater ecosystems were classified into four clusters through the learning process of the self-organizing map. Cluster 1 was characterized by the relatively higher effluent volumes of heavy metals, whereas cluster 4 had lower effluent volumes. The different patterns of the effluent volumes in heavy metals were closely associated with the differences of industrial types, and the changes of effluents of heavy metals reflected the changes in regulations and laws for aquatic ecosystem management.