We analyzed nine benthic foraminiferal species from the Açu Reef belonging to the orders Rotaliida and Miliolida, symbiont-bearing (Rotaliida: Amphistegina gibbosa, Heterostegina depressa; Miliolida: Peneroplis carinatus, Archaias angulatus, Amphisorus hemprichii, and Archaias compressus) and symbiont-barren (Rotaliida: Buccella peruviana, Pseudononion atlanticum; Miliolida: Quinqueloculina lamarckiana). Stable isotopes measured on individual tests display a large intraspecific variability (δ18O: ∼1–1.5‰; δ13C: ∼2–3.5‰) that is not associated with site location, sampling season, or water depth. Positive correlation between δ13C and δ18O values is significant in three of the species (A. gibbosa, B. peruviana, and Q. lamarckiana), with a regression slope similar to other marine calcifiers (∼2‰ δ13C/‰ δ18O), perhaps related to the carbonate chemistry of the calcifying fluid. With the exception of A. gibbosa, offsets from δ18O equilibrium, when distinct, tend to be positive. Offsets from δ13C of ΣCO2 of sea water are negative for two of the rotaliids (A. gibbosa and H. depressa) and positive for three of the miliolids (P. carinatus, A. angulatus, A. hemprichii), with non-symbiont-bearing species of both orders being close to the sea water values (∼ 1.3–2‰). These δ13C differences are consistent with calcification pathways of rotaliids versus miliolids, with the former drawing carbon from an internal pool and the latter from ambient seawater. Our study contributes a large data set that illustrates the importance of vital and abiotic effects on the stable isotopic composition of large benthic foraminifera in a tropical continental shelf, limiting their applicability as paleoenvironmental tracers.