Weekly changes of water environments and phytoplankton community with the salinity gradients were investigated at Gyoungpo Lake from April to November in 1998 and 2012. Underwater crossam in Gyoungpo Lake was removed in 2004. Thereafter, average salinity of Gyoungpo lake increased from 7.5 ppt in 1998 to 20 ppt in 2012. A total of 99 and 80 species of phytoplankton was observed from the sampled in 1998 and 2012, respectively. The number of common species during the 2 separate years was 40. Transparency, SS, NO3-N concentration and N/P ratio in 2012 were lower than those in 1998. During the period of water shortage (April, May) of 2012 transparency decreased due to decreased salinity and increased SS and Chl. a. Correlation coefficients between species and community scores of DCA ordination based on data matrix of the phytoplankton revealed larger variation among sampling seasons in 1998 than in 2012. The increase of seawater influx and conversion rates following the removal of the underwater crossbeam might explain such a differential variation. Gymnodium sp., Peridinium sp., Prorocentrum sp., Nitzschia longissima, Schroederia setigera, Lyngbya sp., Asterococcus limneticus, Asterococcus superbus and Cyclotella meneghiniana were found to well adapt at the high salinities in 2012. Comparatively, Asterrionella formosa, Nitzschia frustulum, Chlorella ellipsoidea, Scenedesmus bijuga and Scenedesmus ellipsoideus were observed at lower salinities in 1998. Two quite contrasting phytoplankton communities were found in the two seasons of a year, spring with limited precipitation and summer, the flood season.