Like nature’s diary, sediment cores record an ecosystem’s history layer by layer, preserving information on past climates, ecological changes, and human activities. These time capsules reveal environmental shifts over thousands of years through fossils like diatoms, single-celled algae that serve as powerful bioindicators of water quality. Diatoms are sensitive to changes in salinity, pH, and nutrient levels and provide insights into past and present aquatic conditions. Changes in species composition within sediment layers highlight ecological transitions, while chemical signals, such as heavy metals and nutrient levels, trace human impacts like industrialization and agriculture. Radiocarbon dating and isotopic techniques establish a timeline of these events, offering guidance for future ecosystem management. Mangrove ecosystems in Demak, Central Java, have faced severe degradation since the 1980s due to agricultural and aquaculture expansion, leading to coastal abrasion. Rehabilitation efforts since 2012 have supported natural regrowth, gradually restoring these critical habitats. This study focuses on Bedono Village, analyzing land-use changes, diatom distribution, and sediment records to understand environmental shifts and promote sustainable coastal management. Diatom analysis revealed freshwater species dominance (49%), followed by marine (38%), freshwater-marine (9%), and brackish (4%) taxa, reflecting adaptations to diverse salinity gradients. Conventional methods identified 140 species, while eDNA metabarcoding highlighted 20.3% of Bacillariophyta and other non-diatom taxa. These findings underscore diatoms’ ecological plasticity and their critical role in monitoring environmental changes, offering valuable insights for the conservation and restoration of mangrove ecosystems.