A recent topic of interest within ecology is ecosystem services that are importantly connected with biodiversity. Biodiversity is a fundamental component of ecological studies and has been the subject of many studies worldwide. However, studies on the diversity and distribution of freshwater fish were not undertaken in earnest until 2000, and the number of internationally available studies is therefore still limited. In this study, we used data from “The Survey and Evaluation of Aquatic Ecosystem Health (hereafter SEAEH)” within the framework of which whole water systems on the Korean peninsula are annually monitored to investigate and determine the current status of the diversity and distribution of freshwater fish, as well as to elucidate major factors impacting freshwater fish. A total of 130 species from 28 families were identified at around 953 sites in the SEAEH investigation of 2014. The species Zacco platypus (relative abundance: 28.2%) and Z. koreanus (19.3%) were identified as the most abundant species on the Korean peninsula, and besides these 20 endangered species, 51 endemic species and 4 exotic species were also collected. Highest (96 species) and lowest (72 species) diversity were identified in the Han River Watershed and the Yeongsan/Seomjin River Watershed, respectively. The mean endemic rate was 32.7%, which is higher than the previous rate determined in 1995. The exotic species Micropterus salmoides, Lepomis macrochirus and Carassius cuvieri were found in the whole river system except north Yeongdong, whereas Oreochromis niloticus occurred only at three sites due to the cold water temperatures in winter. Totally, 28 species were found to be translocated to different water systems not connected with known original habitats, most translocations occurring in the Nakdong River and the Yeongdong region. Among the translocated species, Opsariichthys uncirostris amurensis, and Erythroculter erythropterus were dominantly distributed in the mid- to lower reaches of Nakdong River where they may be harmful to the native fish assemblages due to their strong predation. The construction of weirs in connection with the “4 River Project” generated changes in fish assemblages before, during and after the project, resulting in altered habitat condition. Especially, a decrease in the number of endemic species and an increase in the abundance of lentic species were seen. Human-induced global warming will allow exotic species requiring high water temperatures to adapt to the environmental conditions of the Korean peninsula, which may enhance the diversity of native fishes and create changes in distribution. For the establishment of realistic and efficient management and protection strategies for Korean freshwater fish, SEAEH, which produces fundamental and quantitative data for Korean streams, is an important and necessary tool.