Cebong Lake is one of several lakes in Indonesia located in Sembungan Village and formed by volcanic activities from the Dieng plateau, Wonosobo. Cebong Lake is heavily used by local communities for irrigation, tourism, and the local community’s needs. Water usage will have an impact on lake productivity and fish production. This study aims to determine the environmental changes in Cebong Lake that may have occurred in the past by analyzing the structure community of diatom that composes vertically using 5-65 cm samples sediment of Cebong Lake (interval 5 cm, 13 samples). Methods used for sample treatment include: preparation, digestion, identification of diatom, and enumeration. The result obtained are analyzed using the relative abundance and ecosystem indices. The result found 171 species of diatom belonging to 41 genera, total diatom abundance is 702.975 ind.gr, Diversity index value (H’) ranges between 3.10-3.80, Evenness index value (E) ranges between 0.42-0.70, Dominance index value (D) ranges between 0.03-0.09. Based on Bray-Curtis analysis, Cebong Lake is divided into 2 zones, namely: zone 1 (40-65 cm layers) describes as oligo-mesotrophic waters, and zone 2 (5-35 cm layer) describes as meso-eutrophic waters.