To investigate the changes of dominant species of benthic macroinvertebrates according to the changes of temperature and precipitation, we surveyed twenty sites of the main Seomjin River in May and September in 2013 and 2014. The temperature, precipitation, water quality factors and substrate composition, which are important factors in benthos habitat environment, were collected and measured. The average temperature of the Seomjin River increased by 0.2℃ in 2014 compared to 2013, and the temperature increased from upstream to downstream, showing a difference of more than 3℃. Also, the annual cumulative precipitation (ACP) was increased toward low latitude. The temperature of Seomjin River increased more than twice in September (21.7~24.5℃) after rainfall compared to May (7.6~11.3℃) before rainfall, and CP (cumulative precipitation) increased about 3 times before rainfall (263 mm~287.5 mm) and after rainfall (756.3 mm~882 mm). Due to washing effect by summer precipitation, total number of species and individuals for benthic macroinvertebrates were higher in May than in September. Chironomidae sp. and Choroterpes altioculus were dominated in May, Ecdyonurus levis, Macrostemum radiatum and Choroterpes altioculus were dominated in September. As a result of correlation analysis between community indices and environment factors, it was found that there is a high correlation with boulder and sand among substrate compositions. According to the results of cluster analysis based on temperature, CP and the dominant species of benthic macroinvertebrates in Seomjin River, it was divided into two groups following temperature and CP, and the dominant species and geographical position were reflected and divided into detailed groups.