The Itajaí-Açú and Camboriú rivers are the main important water suppliers for domestic and agroindustrial use in Itajaí and Balneário Camboriú cities in southeastern coast of Brazil. The waste dispoasal by human activities in these estuaries may result in poor water quality and even prevent its use for these activities. In order to evaluate the effects of the human activities upon the estuaries water quality, this study was carried out to evaluate and compare the surface water quality in both estuaries, using a toxicological bioassay to mesure the effect of these waters in growth of marine microalgae Skeletonema costatum (Bacillariophyceae). The samples were colletcted from august of 2003 to march of 2004 in every two weeks at CEPSUL/IBAMA pier (in Itajaí-Açú estuary) and turistic pier (in Camboriú estuary). The physical and chemical characteristics of the samples were determined in situ. The samples were taken to laboratory and frozen for further use. After conducing the bioassay, the results show an increase in algal growth due to excess of nutrients in the samples of both estuaries. This result indicates water eutrophication, as reported in other studies. No effect in the growth of the species was observed for the samples collected in summer months. The samples of march of 2004 from Camboriú estuary were toxic to S. costatum. This result may be due to the disposal of treated wastewater from Balneário Camboriú wastewater treatment plant in the surface river water. The observed concentration effect (CEO) obtained for the samples of march were almost 50%. The CE50 calculated was 96,17% for one sample of march. In the present work, the use of microalgae toxicity test for mesure toxicity in environmental samples and its use as water eutrophication indicator were confirmed.