The spatio-temporal variation of the phytoplankton community structure and the environmental factors that affect its distribution and the changes in Homa Lagoon were examined. Sampling took place monthly at four stations between December 2006 and December 2007. During the study period, a total of 58 taxa of which 52 were used as active taxa in the numerical analysis (relative abundance > 1%) were from four algal classes, Cyanophyceae, Dinophyceae, Bacillariophyceae, and Euglenophyceae. In general, the most important groups were diatoms and dinoflagellates in terms of species numbers and abundance. The mean Shannon-Weaver's diversity index (H') and Pielou evenness index (J') values were 2.35 and 0.83, respectively. An abundance of the bloom of certain phytoplankton species, especially Cylindrotheca closterium and Navicula sp., was thought to be the cause of the low diversity index and evenness values. Although nitrogen was thought to be limiting in temperate regions, phosphorus was a limiting factor on the phytoplankton growth in the Homa Lagoon because of the correlation between the abundance and NIP ratio. The relationship between the phytoplankton communities and 10 environmental variables were researched using a canonical correspondence analysis (CCA). According to the Monte Carlo unrestricted permutation test, the temperature and nitrate concentration were the most important variables in accounting for species distribution.