Rivers are essential ecosystems, yet anthropogenic impacts, including agricultural runoff, industrial discharges, and urban wastewater, have significantly degraded water quality. Eutrophication, driven by excessive nitrogen and phosphorus inputs, poses severe ecological threats by triggering algal blooms and depleting oxygen levels. To address these challenges, it is crucial to investigate ecological indicators that can provide insights into past and present water quality. This study explores diatom assemblages as bioindicators to reconstruct historical changes in water quality and environmental conditions. Sediment cores were collected using a Russian corer from two sites along the river and analyzed for diatom species diversity and abundance. A total of 100 and 105 diatom species were identified in the Agricultural (TA) and Mangrove (TM) areas, respectively, revealing taxa that were both overlapping and site-specific influenced by local conditions. The analysis showed a dominance of benthic diatoms, indicative of nutrient-rich conditions and eutrophication, along with planktonic species affected by hydrological fluctuations. Cluster and stratigraphic analyses using indices like Shannon-Wiener and Bray-Curtis uncovered temporal and spatial variations in species composition, reflecting the impacts of agriculture, land-use changes, and pollution. Key diatom species, such as Nitzschia palea, Fragilaria crotonensis, Melosira varians, and Cyclotella meneghiniana, served as indicators of eutrophic conditions and anthropogenic pressures. The findings another valuable insights for future restoration efforts, emphasizing the importance of diatom-based monitoring in managing and improving riverine ecosystems.