This study analyses diatom assemblages from a Nile Delta core (B-1) to probe Holocene hydroclimate changesand their influence on the ecological habitats of the delta coast, with a further focus on the effects of relative sea-level rise. We found that the freshwater diatom Aulacoseira granulata varied in tandem with hydroclimate pulses in the Nile watershed, driven by the shift of the Intertropical Convergence Zone (ITCZ), therefore serving as a proxy for palaeo-Nile flow. Based on the ecological affinities of diatom taxa, we defined 5 diatom assemblages (I-V). Assemblage I (>10.0-8.5 ka BP) shows high A. granulata abundance (60–80%), implying peak Nile flow during the African Humid Period (AHP), at least 3 times greater than that of the recent past. Assemblage II (8.5-7.5 ka BP) sees decreased A. granulata (20–40%) and emergence of freshwater diatoms with benthic-oligotrophic characteristics (e.g. Epithemia gibba), suggesting reduced Nile flow and a delta estuary where the habitat became shallower with lower nutrient content. Assemblage III (7.5-6.0 ka BP) shows A. granulata resurgence (50–80%), reflecting Nile hydroclimate variability post-AHP due to the migration of the Intertropical Convergence Zone (ITCZ). The high-resolution- diatom spectra of B-1 also revealed major habitat changes, from saline to fluvial-dominated environments, around 6.0 ka BP. Assemblage IV (6.0-3.2 ka BP) indicates a notable Nile flow decline and freshwater community proliferation, coinciding with coastal habitat expansion and delta progradation due to RSL stablisation and basin-wide aridification. Assemblage V (3.2-2.0 ka BP) is marked by drought-tolerant diatoms (Nitzchia amphibia, Hantzschia amphioxys and Cavinula cocconeiformis), indicating intensified aridification.