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• Extensive Middle Miocene fining in southward clastic sequences were deposited in the north of East Java. • Two newly identified turbidite fans exhibit opposite source directions based on 3D seismic data. • The formation of the turbidites fans were predominantly controlled by the paleotopography of the Early Miocene and intense regional tectonic events. • East Java was in a laterally neritic to bathyal environments with occasionally exposed volcanoes during the Middle Miocene. East Java, on the southeastern margin of the Sundaland Shelf, is an ideal and pilot location to study paleogeographic changes due to the interactions of the Eurasian and the Indian-Australia plates. Many studies have been conducted; however, some issues remain poorly understood, such as the initial compression stage and associated paleogeography of East Java. Here, we report newly acquired high-resolution seismic data and drilling wells in the area of the Madura Strait. We systematically reconstruct a three-dimensional model on the paleogeography of East Java in the Middle Miocene in combination with others' results. Different depositional environments and characteristics of the related lithofacies observed on both sides of the Middle Miocene volcanic arc imply that weak subaerial and subaqueous volcanism existed in East Java. The extensive Ngrayong fining in the southward clastic sequences, located north of the mentioned volcanic arc, were deposited in a bathyal marine environment, which showed an oversteepening slope and basinal characteristics with outer neritic to bathyal facies within the present-day Kendeng Zone and Madura Strait area. This differs from the northern region of the present-day Rembang-Madura Inversion Zone and the northern offshore region of East Java, which were deposited in a transitional and neritic marine environment. We identified two new turbidite fans showing opposite source directions based on 3D seismic data within the Madura Strait area. Four controlling factors contributed to the formation of the Ngrayong turbidite fans, including the paleotopography of the underlying Kujung Formation, short-term intense regional tectonic events, high rates of sediment supply and occasional volcanic activity. [ABSTRACT FROM AUTHOR]