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Indonesia, with its vast waters, is home to many islands of ecological, conservation, and navigation significance, including Pulau Pramuka, the capital of the Administrative Regency of Kepulauan Seribu. This study analyzes temporal variations in Langkalangka Reef near Pulau Pramuka, using bathymetric survey data collected in 2022 and 2023 using Multibeam Echosounder (MBES). A Digital Elevation Model of Difference (DoD) approach was applied to quantify elevation changes, with error budgeting to ensure data accuracy. A comparison of survey methodologies and vertical referencing was conducted to ensure further analysis. The results indicate erosion and sedimentation along the reef slopes of Langkalangka Reef, highlighting the dynamic nature of seafloor topography. These findings emphasize the need for a long-term, more comprehensive and interdisciplinary monitoring approach, with standardized bathymetric surveys.