Pollution of surface freshwaters is one of the main environmental problems that result from antrophic activities. Comprehensive studies concerning water quality, however, demand a general understanding of the related aquatic ecosystems. In particular, water quality can be assessed by analyzing phytoplankton composition and diversity which tend to reflect extreme hydrological pertubations. The present study focus on the qualitative description of microphytoplankton, spatial variability of species composition and the creation of a reference collection of these algae in the Camboriu Watershed (Santa Catarina, Brazil) during summer 2005. Sampling was conducted in 9 stations along the basin. After taxonomic identication of the microphytoplankton, a similarity analysis was applied among all sampling stations. A total of 87 taxa of phytoplankton were identified distributed in classes Cyanophyceae (n= 14), Chlorophyceae (n= 19), Zygnematophyceae (n= 11), Euglenophyceae (n= 8), Bacillariophyceae (n= 34) and Crysophyceae (n= 1). Sampling stations located near the potamon environments showed highest values of total richness and those stations located near the rhithron environments the lowest richness values. The similarity analysis among stations revealed four dissimilar groups, separated into, urban, peri-urban, rural and naturial areas.