We examine the mesoscale structure of the atmospheric boundary layer (ABL), low-level circulation, and trade wind convection over the sub-tropical island of Puerto Rico in mid-summer. Shallow afternoon thunderstorms are frequently seen over the western plains of the island. Observational data include automatic weather station measurements, radiosonde profiles, infrared satellite images, and mesoscale reanalysis data with a focus on the summer of 2006. Satellite microwave radar data (TRMM and CloudSat) indicate that island clouds typically extend just above the −20◦ C level during afternoon hours with reflectivity values reaching 50 dBz. A singular value decomposition of 3-hourly high resolution satellite rainfall maps reveals an island mode. From this a composite is constructed for a group of ten cases. With a Froude number ≈1 the trade winds pass over the mountains and standing vortices and gravity waves are trapped in the meandering wake. The Weather and Research Forecasting (WRF) model at 1-km resolution with 51 vertical layers is used to simulate the short-lived thunderstorms for two cases: 27 June and 20 July 2006. The model correctly locates the convective cells that develop between 1400 and 1700 LST. The shallow afternoon thunderstorms are triggered by surface heat fluxes, confluent sea breezes and a mountain wake. Recommendations for enhanced observations are given.