Marine algal flora and community structure were investigated seasonally at four stations in Busan, in which coastal area and estuary affected by Nakdong river are involved, from February 2011 to October 2011. Total 78 species including 9 of cholophyta, 17 of phaeophyta and 52 of rhodophyta were found during the study period. Maximum and minimum species number were recorded at station 1(57 species) and at 3(32 species). As based on the cluster analysis, grouping pattern between the four stations was significantly affected by season and Nakdong river run off. At station 3 directly exposured on Nakdong river run off, species diversity was relatively low and dominant species were similar throughout four seasons. However, coverage at the station was relatively high because of Ulva bloom. This difference results from salinity and nitrates concentrations closely related with river runoff controlled according to precipitation. Marine algal coverage was high at lower salinity and higher nitrate concentration. In conclusion, the spatio-temporal distribution of benthic marine algae in estuary of Nakdong river was mainly determined by the precipitation and river run off with the seasons, whereas that in coastal area was seasonally affected by general physical, chemical, biological and dynamic factors.