The northern part of the East Java Basin has become a focus of research by earth scientists, among others, because of the existence of hominid fossils and remains of other vertebrate taxa within the Quaternary sedimentary sequence. Fossil-bearing layers are found in the Kendeng Zone, mostly within the well-known Pucangan and Kabuh Formations, which are distributed from Central to East Java. However, not all formations contain vertebrate fossils as well as hominid elements. It is important to consider what factors may have influenced the concentration of vertebrate fossils in those formations. In this study, we describe sedimentary facies at three key field locations: Sangiran, Ngawi, and Mojokerto. Our study indicates that vertebrate remains and hominid fossils mainly accumulated in continental sediments associated with lacustrine and fluvial systems. In this regard, Sangiran and Ngawi B offer the greatest prospect for yielding hominid remains, owing to their unique paleoenvironmental and paleogeographical settings as a highland during the Early–Middle Pleistocene period. Certain parts of the Kabuh Formation in the Mojokerto region also hold high potential, especially those displaying evidence of continental deposition.