Resumo. Abstract: Aim in this paper we investigated how spatial factors and seasonal dynamics influenced the diatom community in a tropical deep environment of low productivity waters in Brazil. Methods we used physical and chemical characteristics of the water and planktonic diatoms from 9 sampling stations during dry (austral winter) and wet (austral summer) seasons (N = 18) as the outline to identify water quality, spatial and seasonal patterns. To evaluate spatially and temporally integrated events from the recent past (approximately the last 5 years before sampling), and the species from diverse habitats of the system, we used diatoms from the surface sediment (top 2 cm, N = 9). Since we used the top 2 cm of surface sediment containing the dead diatoms that were deposited over recent past of the reservoir, seasonal sampling of the sediment was not needed. Results during the dry season heavily silicified long colonial planktonic diatom species associated mainly with higher mixing depth, pH, and transparency dominated the plankton, whereas in the wet season the reservoir became stratified, favoring planktonic solitary diatoms with high surface volume ratios. For the sediment, a general pattern emerged where planktonic species dominated in the deep sections of the reservoir, and the abundance of benthic species in shallow areas near the tributaries increased. Conclusions the diatom assemblages was mainly influenced by seasonal variations and mixing regime. Surface sediment samples provided longer-term information, and revealed habitat differentiation shaping diatom assemblages. Overall, the small centric planktonic Aulacoseira tenella (Nygaard) Simonsen stood out as the most abundant species in the entire reservoir in both, the plankton and the sediment, indicating that size and shape serve as adaptive strategies for buoyancy and nutrient uptake stand as a competitive advantage in deep low productivity environments.