The measurement of sea level height relative to a fixed reference point, such as the geoid or mean sea level, is known as sea surface topography. There are a number of factors that affect it, such as undulation, sea surface height, and tides. Measurement of sea surface topography is very important to understand ocean dynamics. One of the factors that influences the dynamics of the sea is the flow across Indonesia. The Indonesian traffic flow is the mass flow of water from the Pacific Ocean to the Indian Ocean. The difference in pressure between the two oceans is what causes the flow. The purpose of this study is to provide precise information about the sea surface topography in the East Indonesian Sea region during the 2016–2021 period, which is required for various marine applications. This approach involves processing and analysing Jason-3 altimetry satellite data, which provides precise sea level elevation measurements. The data is then used to determine the value of the sea surface topography, which shows the spatial and temporal variations in sea level height in the region. The average sea surface topography value every month from 2016 to 2021 ranges from 1.05m to 1.30m, with the highest value occurring in January 2021 at 1.2542m and the lowest value occurring in February 2016 at 1.0498m. For the accuracy of processing results, data for 2016–2021 is used as training data for model estimation and 2021 as test data. The root mean square error value is 0.0762m. Changes in sea surface topography values tend to increase every year, except for 2019. The decline that occurred in 2019 was caused by the ENSO phenomenon, which had an effect of -0.807 on sea surface topography with an inverse correlation. The findings of this study provide important details about sea surface topography in Eastern Indonesian waters, which can be applied to enhance our understanding of ocean dynamics.