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Mahakam Delta is a delta with unique characteristics. As a result of the continuous sedimentation process, the delta can be said as a complex delta because it has dozens of tributaries that are interconnected and flow into the sea to their estuaries. Mahakam Delta estuary is a meeting place for mixing masses of water from freshwater rivers and high salinity rivers. The aim of this study is to determine the water column stratification seen from the salinity and temperature parameters in the Mahakam Delta estuary. This study uses the ECOMSED model which is run for 40 days (July 7 to August 16, 2018) with tides and river discharge as the generating force. The simulation results show that stratification is predominantly influenced by differences in salinity between the layers. The strongest stratification is located in the upper Mahakam Delta line with a difference in salinity is 8 ppm from surface to bottom layer.