This paper deals with structure and processes in the marine boundary layer along air mass trajectories over and in the vicinity of the cold water tongue of the eastern equatorial Pacific Ocean. The study is based on three NASA P3-B aircraft missions from Guayaquil, Ecuador, part of the NASA Pacific Exploratory Mission-Tropics experiment. The observations were made during September 1996, which is part of the cold season when the lowest sea surface temperatures are expected. The boundary layer and the overlying free troposphere showed several unique features not observed previously. While the boundary layer was advected over the equatorial cold tongue toward the Intertropical Convergence Zone, the overlying free tropospheric air consisted of warm, moist outflow from the South American continent where deep convection was taking place. The specific humidity just above the inversion was typically 1--2 g kg-1 higher than that in the boundary layer. These conditions tend to suppress cloud top radiative cooling and entrainment at the boundary layer top. Over the coldest upwelling areas, shallow thermal internal boundary layers were observed. We discuss changes in cloudiness, sensible and latent heat fluxes, and the scale of turbulence in and above the thermal internal boundary layers, and during the reestablishment of the convective boundary layer upon passing over a warmer sea surface. ¿ 1999 American Geophysical Union