The Quimbo Dam was built over the Magdalena River in 2011 and started functioning in November 2015. In this research the composition of phytoplankton during its first stages of functioning was studied through qualitative-quantitative analysis as well as the relation among the most abundant species and the physicochemical parameters of pH, DO, water Temperature, and conductivity though correlation analysis. Quantitative results of microalgae were analyzed with diversity indexes of Shannon, Margalef, Simpson and, Dominance. A total of 12 Classes, 58 genders, and 84 species, including 8 new registers for Colombia were found. The classes BACILLAROPHYCEAE, CHOLORPHYCEAE and CYANOPHICEAE were the most abundant in species and cells/ml. Eight species represented more than 10% of the total cells/ml in every sample and they are all related with eutrophic conditions. Dissolved oxygen and pH were measured at three different depths in four stations showing a clear tendency to hypoxia. Further studies are needed as well as sustainable strategies of management and monitoring for the dam, to prevent it from reaching a deadline sooner than needed and affecting even more the Magdalena river basin.