Abstract: Lakes are one inland water that has important water resources, covering 72% of the total Indonesian surface water. However, Indonesia faced a water crisis, especially in Java, Bali, and Nusa Tenggara. Even when the pandemic Covid-19 changes to endemic, the striving for clean water is challenging to fulfill the demand. Increasing human population and reduction of the water sources is one of the problems: water quality, sedimentation, eutrophication, the threat of biodiversity, and water quantity which in turn affected lake function for hydropower electricity, irrigation, fisheries, tourism, and socio-cultural activities. On the other side, climate change also threatened the inland freshwater ecosystem and its services. The paleolimnological approach will be discussed as a base for developing sustainable lake management. Protection, conservation, restoration, and sustainable use of the lakes are essential for the integrated management plan for each lake, with the pilot project of Rawapening Lake. This implementation paleo reconstruction had been applied in Balekambang Lake, a small ancient lake in Dieng Plateau that is threatened to be extinct. The record of flooding, eruption, and deterioration of water quality histories well preserved in the sediment.