Results from sediment trap experiments conducted in the seasonal upwelling area off south Java from November 2000 until July 2003 revealed significant monsoon‐, El Niño–Southern Oscillation–, and Indian Ocean Dipole–induced seasonal and interannual variations in flux and shell geochemistry of planktonic foraminifera. Surface net primary production rates together with total and species‐specific planktonic foraminiferal flux rates were highest during the SE monsoon‐induced coastal upwelling period from July to October, with three species Globigerina bulloides, Neogloboquadrina pachyderma dex., and Globigerinita glutinata contributing to 40% of the total foraminiferal flux. Shell stable oxygen isotopes (δ¹⁸O) and Mg/Ca data of Globigerinoides ruber sensu stricto (s.s.), G. ruber sensu lato (s.l.), Neogloboquadrina dutertrei, Pulleniatina obliquiloculata, and Globorotalia menardii in the sediment trap time series recorded surface and subsurface conditions. We infer habitats of 0–30 m for G. ruber at the mixed layer depth, 60–80 m (60–90 m) for P. obliquiloculata (N. dutertrei) at the upper thermocline depth, and 90–110 m (100–150 m) for G. menardii in the 355–500 μm (>500 μm) size fraction corresponding to the (lower) thermocline depth in the study area. Shell Mg/Ca ratio of G. ruber (s.l. and s.s.) reveals an exponential relationship with temperature that agrees with published relationships particularly with the Anand et al. (2003) equations. Flux‐weighted foraminiferal data in sediment trap are consistent with average values in surface sediment samples off SW Indonesia. This consistency confirms the excellent potential of these proxies for reconstructing past environmental conditions in this part of the ocean realm.