A retrospective study is one of the most critical aspects of paleoenvironmental studies on developmental planning and environmental monitoring from a geological perspective. The semi-enclosed bay of Lamong Bay, Surabaya, and Benoa Bay, Bali, was rapidly accelerated physics and ecological development on the national scope. The contrary semi-enclosed marine system is linked to large-scale anthropogenic disturbances. This study provides useful baseline information for stakeholders in preparing disaster mitigation plans. This study was aimed to determine past ecological changes based on the paleoenvironmental analysis in two bays with very different environmental development characteristics. i.e. Lamong Bay, Surabaya and Benoa Bay, Bali. Sampling was conducted in March 2017, including analysis of absolute age and sedimentation rate using the Pb210 isotope and foraminifera recent indexing from short core samples. The Ammonia-Elphidium index (A-E index) and the planktonic/benthic ratio (P/B) were used as a proxy of hypoxia and open ocean flow, respectively. Analysis of foraminifera characteristics showed that the study sites had experienced different ecological changes in the last few decades. Over the past 87 years, Lamong Bay has undergone ecological changes, from the aquatic environment strongly influenced by the open sea and supporting benthic life to shallow oligotrophic waters that cannot supports benthic life. In contrast, Benoa Bay has been shallow for the past 50 years and supports benthic life without the threat of hypoxia due to eutrophication.