The present study was carried out in Castanhão Reservoir, a large aquatic system in the Brazilian semi-arid region that serves multiples uses as water drinking supply and intensive fish-cage aquaculture site. In order to understand the effects of environmental conditions on the spatial and temporal variability of the phytoplankton functional groups (FG) and the main ‘characterizing taxa’, sub-superficial water samples were collected from March 2012 to August 2013, a period distinguished by the continuous drop in reservoir volume due to rainfall shortage. Eighteen functional groups and 102 total phytoplankton taxa were found in the Castanhão reservoir during the study. No significant differences were observed relative to spatial variation of total phytoplankton composition throughout the reservoir (PERMANOVA, P>0.05). On the other hand, according to cluster analysis results, three temporal phases have been identified (Similarity Profile, P<0.05), based on 102 phytoplankton taxa. The ‘characterizing taxa’ was found using the Similarity Percentage procedure (cut-off 90%), being thus defined as those taxa that contributed the most to the similarity within each temporal phase. Nineteen ‘characterizing taxa’ described the Castanhão reservoir, with predominance of those typical of mixing and turbidity conditions. Cyanobacteria dominated through the three temporal phases. According to the redundancy analysis, nutrient availability and water transparency were found to influence the phytoplankton temporal dynamics. The phase I (rainy season) was most represented by Planktolyngbya minor/Pl. limnetica (FG = S1), which reached best performance under strongly decreased phosphate-P concentrations and low water transparency. In phase II (dry season), Romeria victoriae (FG = ?) outcompeted other cyanobacteria probably due the increase in water transparency and decrease in ammonium-N. Finally, in phase III (rainy season) the decrease of water transparency triggered a recovery of shade-adapted cyanobacteria, but at this time mostly represented by Pseudanabaena limnetica (FG = S1). Phase III was also distinctive from the other ones by the highest Nitrate-N and phosphate-P concentrations related to thermocline disruption, which favored an increase in total phytoplankton biomass recorded by the augment of green algae density (FGs = X1, J and F). We concluded that the temporal dynamics of phytoplankton composition was associated to environmental changes in Castanhão Reservoir from 2012 to 2013, which were driven by seasonal climate variation from region (rainy/dry seasons), as well as, by the reduction in reservoir volume that resulted in the disruption of the thermocline, water mixing and an increase in inorganic P and N.