THE western equatorial Pacific has an important role in the El Nino/Southern Oscillation climate cycle 1,2, and sea-surface temperature anomalies in this area are known to affect the global atmospheric circulation 3. Little is known, however, about the factors that control the response of the upper ocean, and hence sea surface temperature, to changes in atmospheric conditions. Here we present observations of the density and current structure of the upper layers of the western equatorial Pacific Ocean. We observed frontal features with temperature differences of 1-degrees-C extending from the surface down to a depth of 150 m, a strong salinity front associated with a surface convergence, and interleaving of high- and low-salinity waters in 10-m-thick layers that extended for several hundred kilometres in the north-south direction. The large spatial and temporal variability in temperature and salinity observed must influence heat transport, and hence the ocean response to atmospheric forcing (in particular the response to westerly wind bursts, which are thought to be precursors to an El Nino). We estimate the horizontal diffusion coefficient of the interleaving, which indicates that the observed layering may contribute to horizontal mixing within the thermocline.