Phytoplankton composition in lotic environments has received less attention than that of lentic environments. The aim of the present study was to describe the micro-phytoplankton of the Contas River, which is one of the five most important water bodies in the state of Bahia, Brazil. Collections were carried out at 28 sampling sites at three-month intervals over a three-year period between December 2007 and September 2010. The micro-phytoplankton community was represented by 198 taxa distributed among Bacillariophyceae, Coscinodiscophyceae, Cyanophyceae, Fragilariophyceae, Chlorophyceae, Euglenophyceae, Dinophyceae, Cryptophyceae, Chrysophyceae and Xantophyceae. Geitlerinema amphibium (C. Agardh) Anagnostidis, Planktothrix agardhii (Gom.) Anagnostidis and Komárek, Pleurosira laevis (Ehrenberg) Compère and Ulnaria ulna (Nitzsch) P. Compère occurred in all samples. The majority of species (n = 111; 56.06% of the taxa) were classified as rare in the Contas River, as these organisms were only recorded during one or two months.