The benthic ecosystem in the coastal area near nuclear power plants is affected heavily by thermal discharge, but only a limited number of studies have investigated long-term changes in community structure. In addition, little is known about the environmental factors required for good benthic polychaete habitat in areas affected by thermal discharge with variety of sediment types. Therefore, this study analyzed macrobenthic community structure over the past 10 years at nuclear power plants operating in the East Sea. In addition, polychaete community structure in a variety of sediment types was studied. In total, 319 species were identified in 2012–2013; the mean density was 3,330 inds./m2, and the mean biomass was 131.96g/m2, which was similar to a 2006–2007 study.Dominant species were different before and after operation of the nuclear power plants and the density of macro invertebrates per station changed substantially after the nuclear plants began operating. The polychaete pollution indicators Spiophanes bombyx and Polydora sp. were dominant only at stations near the nuclear power plants. This could be attributed to changes in sediment type from smaller particles to larger particles shown around the plants. Macrobenthic community structure was divided into group A (<30 m depth) and group B (>30 m depth) in 2012–2013. The macrobenthic community structure of group A was not different before and after operation of the plants but seasonal changes were observed. Changes made in thermal discharge played a bigger role than other environmental factors. Therefore, fluctuations in the thermal discharge could cause changes in the macrobenthic community structure in thermal discharge regions, thus, requiring constant monitoring of conditions. The polychaete community structure was studied in two thermal discharge areas, Uljin and Gori, and one reference area (Hupo) from August 2006 to February 2013. In total, 283 species were identified; the polychaete density was 4,912 inds./m2; the primary dominant species were S. bombyx, Magelona japonica, and Sternaspis scutata. Spiophanes bombyx was the most dominant species in sandy sediment from the Uljin and Hupo regions; however, M. japonica was the dominant species in the muddy sediment at Gori. Two other dominant species, Lumbrineris longifolia and M. japonica, dominant species in the East Sea, were nearly absent in areas around intake holes and at the discharge of the nuclear power plants. Polychaete species were affected by the artificial environmental disturbance around the intake and discharge zones of the nuclear power plants. A polychaete cluster analysis showed that total organic carbon, sediment grain size, and sediment type were the major environ mental factors associated with community structural changes. The polychaete community structure was affected by the thermal discharge around the intake and discharge areas, but only limited to a narrow region, whereas the other areas were affected largely by other environmental factors, such as total organic carbon, sediment grain size, and sediment type.