In the fishing industry, in order to manage fishing resources effectively, it is important to adopt measures for aquatic resources based on an understanding of the current ecological conditions of an area. To help in this regard, we as the staff of the Shiga Prefecture Fisheries Experiment Station collected and surveyed fish and crustaceans from Lake Biwa and it's surrounding rivers in 1994. We could confirm the existence of most of the fish and crustaceans in Shiga Prefecture; however, it is feared that the ecosystems in these waters are changing. According to our study, depending on the area surveyed, we found that there was a small population of several species while there was an increase in population of other species which were normally fewer. Furthermore, we found that a diverse environment is essential for a variety of species to co-exist.