Resumo. Abstract Aim: A series of dams along the course of a river forms a complex cascading reservoir system. The interconnectivity of the dams is perceived with the reduction of turbidity and phosphorus and the increase of specific richness throughout the system. Designing a management system that promotes the integration of biotic and abiotic data is essential to these resources of recognized importance for the population, the country's power generation and watersheds management. The Jacuí River is an important water resource in the state of Rio Grande do Sul, along its upper course, five water reservoirs comprise a cascade system tapped for energy generation and agriculture, but the effects on the phytoplankton community of cascading dams are still unknown. Thus, the present study aimed to investigate spatial and temporal patterns of phytoplankton associated with climatological and limnological characteristics of the Ernestina and Itaúba water reservoirs, located in the upper Jacuí River, RS, Brazil. Methods Sampling campaigns were carried out seasonally from January 2012 to February 2013, with four sampling stations within each dam and at three different depths. The sampling units were determined according to the three zones of the reservoir: river areas, transition and lake. Results: A total of 91 phytoplankton species were identified in Ernestina and 130 in Itaúba. There was no significant difference between vertical and horizontal patterns, since the community responded to seasonal changes and the specific characteristics of each dam. Conclusions The specific richness and water transparency increased downstream of the system and changes in water retention time were important for cell density and composition.