The relationships between planktonic foraminifera in the upper 2000 m of the water column and those in sediment traps and deep-sea sediments of the Panama Basin were investigated as part of the Composition, Flux and Transfer Experiments (CFATE) and the Sediment Trap Intercomparison Experiment (STIE) July–Dec. 1979. Planktonic foraminifera larger than 333 μm, sampled during the July–August trap deployment cruise, occurred most abundantly in the euphotic zone with maximal populations associated with the chlorophyll and primary production maxima both located in the upper thermocline just below the mixed layer. Juvenile abundances exceeded those of the >333 μm adults by 3–4 orders of magnitude and their depth distribution systematics indicated that most foraminifera reproduction occurs prior to sinking of the adults from the euphotic zone. Macroscopic aggregates and fecal pellets were identified as major carriers of smaller sized shells from the euphotic zone. During the July–August cruise, the species changed from an assemblage dominated by G. theyeri to one dominated by G. ruber; the live G. theyeri population sank passively from the euphotic zone in early August with a mean settling speed of 150 m day −1 while the G. ruber population grew in. The abundance of empty shells of all species in the upper 200 m varied by a factor of 40 during the deployment cruise and peaked on July 30, 1979. This variability was reflected in foraminifera collection rates of sediment traps deployed at 305 m for 24- and 6-h periods. The trap and watercolumn data were combined to calculate mean sinking speeds (>333 μm fraction) of several dominant foraminiferal species ( G. ruber and G. theyeri, 500 m day −1; G. dutertrei, 2000 m day −1). Size and weight analysis of empty shells from plankton tows yielded values of empty shell density (calculated on a spherical basis using maximum shell dimension) ranging from 0.12 and 0.15 g cm −3 ( G. theyeri and G. ruber) to 0.60 g cm −3 ( G. dutertrei). These speeds and shell densities were found to be consistent with the laboratory sinking experiments of Berger and Piper (1972) and Fok-Pun and Komar (1983). It was concluded that shell fluxes through the water column may be calculated with reasonable accuracy using a modified version of the Bishop et al. (1977) settling model and empty shell size distribution data from pump and plankton tow collections. The Fok-Pun and Komar (1983) settling model is recommended for future modelling efforts but requires a more extensive set of measurements of each foraminiferal specimen to be made. The interpretation of foraminiferal flux profiles, based on the collections of sediment traps, plankton tows, and pumps deployed on time scales shorter than several days, must take into account the very short residence times of empty shells in the water column and short term temporal variability in empty shell production rates. Populations of >333 μm foraminifera sampled in Nov.–Dec. 1979 were reduced by a factor of six relative to the July–Aug. values. The cruise-to-cruise differences were due to reduced primary production and greater mixed layer depth. Planktonic foraminifera were well preserved in sediment traps deployed for 112 days at 665, 935 and 1770 m, although aragonitic pteropod shells were partially dissolved. The fluxes of many species into the 935 m trap could not be explained based on the standing stock data from the July–August cruise alone and it was noted that species fluxes during STIE were comparable to or exceeded maximal values measured by Thunell and Reynolds (1984) in bi-monthly time series traps deployed at the same location during the whole of 1980. The moored trap data could only be explained by higher mean foraminifera shell fluxes in the interval between trap deployment and recovery, consistent with the Bishop and Marra (1984) model of primary production and carbon flux at the STIE site. Primary differences between core top samples and trap samples, were explained by the loss from the sediments of dissolution prone species, G. theyeri and G. ruber leaving an assemblage dominated by the dissolution resistant species, G. dutertrei.