The Kutai Basin (East Kalimantan, Indonesia) contains a rich and well-preserved Miocene fossil record of small patch reefs that developed under the influence of high siliciclastic input associated with the progradation of the Mahakam Delta. In this study, we reconstruct the biodiversity and paleoenvironments on one of these delta-front, mixed carbonate-siliciclastic systems that developed at the Serravallian–Tortonian boundary near the city of Samarinda. In two newly exposed sections, we analyzed the sedimentology and distribution of the main fossil biota including corals, foraminifers, coralline algae, and bryozoans. Seven facies are herein defined, including two dominated by platy corals and two by larger benthic foraminifera. Facies distributions were driven by changes in depth and variations in terrigenous input within a range of delta-front habitats. Despite the turbid conditions, fossil assemblages are highly diverse, including 69 coral species and 28 bryozoan species that occur in coral-dominated facies. Crustose coralline algae were mainly associated with the coral-dominated facies. Larger benthic foraminifera showed broader ecological tolerance within the range represented in the studied sections and thus are common in most facies. These diverse patch reef ecosystems were able to cope with high siliciclastic input during the early development of the Miocene coral reef biota.