These profiles enabled to evaluate vertical patterns of thermocline, dissolved oxygen, chlorophyll and phycocyanin. Objectives of this work was to understand the occurrence of thermocline associated with bottom anoxia and the vertical distribution of phytoplankton in reservoirs. Three aquaculture areas were monitored from 2014 to 2016, sampling inside each farm, upstream and downstream. Relationship of climate and water outflow upon stratification were also evaluated , as well as the applicability of in situ fluorometry for monitoring cyanobacteria . Results showed the predominance of stratification conditions with bottom anoxia in all sampling seasons for at least one sampling site. Maximum values of pigments in subsurface layers were common , indicating underestimation by surface water samplings, traditionally used for the trophic state ev aluation of aquatic environments, as chlorophyll maximum frequently was registered in subsurface layers. The stratification strength is variable and it was not evidenced that hydrological regime, air temperature and precipitation had no significant influence on the thermal stratification and bottom anoxia. Thus, the use of real time water monitoring technology proved to be a useful and important tool to follow the changes in the vertical structure of reservoirs. Sites with high oxygen in surface frequently had bottom anoxia extended several meters up in the water column, posing severe risks to cage aquaculture. In addition, it became evident the need to access vertical distribution of oxygen and phytoplankton to proper evaluations of water quality and environmental risks for cage aquaculture in large hydroelectrical reservoirs.