This dataset contains the relative abundance of diatom taxa identified in 68 sediment samples collected at 0.10 m intervals from core NGR07, from Lake Pacú, in the lower Negro River region of the Central Amazonia. The diatom assemblages were analyzed to reconstruct changes in aquatic conditions associated with flood pulse oscillations during the mid- to late Holocene. Approximately 500 valves were counted per sample using light microscopy, and taxa were identified based on microstructural features, supported by regional diatom atlases. The dataset includes both periphytic and planktonic forms, reflecting lake-level variations since the mid-Holocene. Diatom diagrams and zonations were generated using Tilia and CONISS software.

Further method/device information:Instrument Type: Light microscope, Zeiss, Axiolab 5 with Axiocam 208 color camera (430037-9110-000, Microscopy GmbH).Preparation Method: Sediment sample volumes were measured using a stainless-steel volume gauge, producing cylindrical pellets of 3 cm³. Each pellet was treated with 30% hydrogen peroxide (H₂O₂) at 50 °C to oxidize organic matter, followed by 10% hydrochloric acid (HCl) to remove carbonates. Lycopodium spore tablets were added for concentration estimation. Samples were washed by repeated decantation with distilled water until reaching neutral pH. Permanent slides were prepared by drying thematerial on coverslips and mounting with Entellan®.Counting Method: At least 500 diatom valves were counted per sample under 1300× magnification. Identification was based on morphological features of the silicified valves, following Rodrigues et al. (2023, doi:10.1016/j.dib.2022.108855 ; 2023 doi:10.1016/j.dib.2023.109033).