The salinity variability of the upper ocean is influenced by surface heat, momentum, and freshwater fluxes, which are in turn affected by atmospheric conditions. It is necessary to accurately measure these surface fluxes within their atmospheric environment to understand the linkages between rain events and the resulting upper-ocean salinity balance that occurs at cloud scales. We describe a comprehensive set of atmospheric and oceanic data collected during the second Salinity Processes in the Upper-ocean Regional Study (SPURS-2) experiment in the tropical eastern Pacific Ocean. These measurements included direct estimates of heat, moisture, and momentum fluxes using direct covariance flux systems on R/V Roger Revelle and a 3 m discus buoy. These are the first successful direct measurements of evaporation from a buoy over an extended period. The atmospheric moisture budget is estimated from a combination of data, including measured freshwater fluxes, upper air sounding data, and satellite data. This analysis reconfirms the important role of moisture convergence beneath the Intertropical Convergence Zone in this region. We perform an analysis of the near-surface vertical salinity structure and its relationship to these surface fluxes, highlighting the roles of stabilization by solar insolation and precipitation and the effects of rainfall on mixing of the upper ocean.