The distribution of modern benthic foraminifera is studied from offshore mixed carbonate-siliciclastic settings of Brunei Darussalam located in northwestern Borneo (South China Sea). The sediments were collected from 17 sites (i.e., shallow reefs, sunken wrecks, and two depth transects). A total of 231 species were identified from 8 to 63 m water depth. We conducted several analyses to understand the patterns of faunal composition, including: (1) Cluster analysis and Principal Component Analysis together with correlation to define relation among the sites; (2) Diversity indices, such as Shannon Index and Fisher's Alpha Index to assess diversity patterns at sites; and (3) Foram Index (FI) to determine whether the water quality indicates conditions that support reef growth. The most abundant foraminiferal groups from the reef and most wreck samples are larger benthic foraminifera (LBF), especially Calcarinidae and Amphisteginidae, whereas in the muddier sites the most abundant are smaller benthic foraminifera (SBF) with the genera Pseudorotalia and Asterorotalia. Certain species from the groups have shown patterns that do or do not correlate with depth and clay content.