Borneo's geologic and paleontological history remains poorly understood because of the lack of outcrops and difficulties with dating. Urban development around the city of Samarinda has produced over four kilometers of well-exposed stratigraphy depicting the progradation of the ancient Mahakam river delta across the Samarinda area, which includes slope, shelf, and deltaic deposits (clastic and carbonate). Previous studies have preliminarily dated the succession as middle Miocene, but reworking and the scarcity of diagnostic fossils make dating difficult. In this paper, an integrated stratigraphic age model has been constructed for the middle Miocene of the Samarinda region with a combination of magnetostratigraphy, sequence stratigraphy, and biostratigraphy (nannofossil, planktonic foraminifera, and larger benthic foraminifera). This age model provides improved temporal constraints for part of the Mahakam Delta succession. It also helps to place the pattern of biodiversity changes seen in Indonesian reef communities into a better time perspective, and permits more accurate sedimentation rates to be determined. It may also serve as a reference point to compare other Neogene sections in Southeast Asia. The two reef complexes at Samarinda, the Batu Putih and the Stadion section, are magnetostratigraphically dated at ∼ 15 Ma and 11.6 Ma, respectively. The new chronology for the Samarinda succession shows that the Mahakam Delta went through a major phase of buildout and progradation during the middle and earliest late Miocene, during which time progradation across the former shelf break took place in the Samarinda area.