Horizontal and vertical distributions of δ~(18)O and δ~(13)C were investigated in shells of four planktonic foraminiferal species, Globigerinoides ruber, Globigerinoides sacculifer, Pulleniatina obliquiloculata and Neogloboquedrina dutertrei, from a total of 62 core-top sediment samples from the Indonesian throughflow region. Results were compared to modern hydrologic conditions in order to explore potential of proxies in reconstructing fluvial discharge and upper ocean water column characteristics in this region. Our results show that, in the Makassar Strait, both of depleted δ~(18)O and δ~(13)C of these four species were linked to freshwater input. In the Bali Sea,however, depleted δ~(18)O and δ~(13)C for these species may be due to different reasons. Depleted δ~(18)O was a result of freshwater input and as well influenced by along-shore currents while depleted δ~(13)C was more likely due to the Java-Sumatra upwelling. Comparison of shell δ~(18)O records and hydrographic data of World Ocean Atlas 2005 suggests that G. ruber and G. sacculifer calcify within the mixed-layer, respectively at 0–50 m and 20–75 m water depth, and P. obliquiloculata and N. dutertrei within the upper thermocline, both at 75–125 m water depth. N.dutertrei calcifies at slightly deeper water depth than P. obliquiloculata does. In general, δ~(13)C values of both G.ruber and G. sacculifer are larger than those of P. obliquiloculata and N. dutertrei at all sites, possibly related to depth habitats of these species and vertical distribution of nutrients in the Indonesian throughflow region. Horizontal and vertical distributions of δ ~ (18) O and δ ~ (13) C were investigated in shells of four planktonic foraminiferal species, Globigerinoides ruber, Globigerinoides sacculifer, Pulleniatina obliquiloculata and Neogloboquedrina dutertrei, from a total of 62 core-top sediment samples Results from compared to modern hydrologic conditions in order to explore potential of proxies in reconstructing fluvial discharge and upper ocean water column characteristics in this region. Our results show that, in the Makassar Strait, both of depleted δ ~ ( 18) O and δ ~ (13) C of these four species were linked to freshwater input. In the Bali Sea, however, depleted δ ~ (18) O and δ ~ (13) C for these species may be due to different reasons (18) O was a result of freshwater input and as well influenced by along-shore currents while depleted δ ~ (13) C was more likely due to the Java-Sumatra upwelling. Comparison of shell δ ~ (18) O records and hydrographic dat a of World Ocean Atlas 2005 suggests that G. ruber and G. sacculifer calcify within the mixed-layer, respectively at 0-50 m and 20-75 m water depth, and P. obliquiloculata and N. dutertrei within the upper thermocline, both at a depth of 75-125 m. N. Dutertrei calcifies at slightly deeper water depth than P. obliquiloculata does. In general, δ ~ (13) C values ​​of both G. ruber and G. sacculifer are larger than those of P. obliquiloculata and N. dutertrei at all sites, possibly related to depth habitats of these species and vertical distribution of nutrients in the Indonesian throughflow region.