Larger benthic foraminifera (LBF) show great tolerance to environmental conditions and occur in shallow, tropical marine habitats and depositional settings, including mixed carbonate–siliciclastic (MCS) systems; the latter are characterized by deposition of carbonate producers under the influence of a terrigenous input. In this study, MCS system deposits near Samarinda and Bontang in East Kalimantan (Indonesia) are investigated. These include 10 sections divided into three groups based on their geological age and geographical position: Bontang sections (Burdigalian age), Batu Putih sections (Langhian age), and Stadion sections (Serravallian/Tortonian boundary). Recent studies propose different depositional environments for the studied MCS systems and initiated a need for discrimination among such conflicting interpretations. We apply cluster analysis, detrended correspondence analysis, and analysis of similarity to the LBF assemblage data matrix and interpret the results with predictions from the trophic resource continuum model. The significant differences in LBF diversity and assemblage composition confirm that MCS systems of East Kalimantan developed in differentiated environments. The Batu Putih sections were interpreted to develop in the widest range of depositional environments, from delta front to shelf edge reefs. The Bontang sections were deposited in a narrower range of depositional environments compared to the Batu Putih sections, while the Stadion sections developed in the most restricted environment, under highest terrigenous input in delta front settings.