The climate of the Southeast Pacific (SEP) involves important feedbacks between atmospheric circulation, sea-surface temperature (SST), clouds, oceanic upwelling and ocean heat transport. In particular, the effects of ocean mixed layer and atmospheric boundary layer coupling such as SST affect the stability of the atmospheric boundary and concomitantly alter the surface stresses and surface heat fluxes and, in turn, the altered fluxes affect the ocean eddy statistics. We examine the air-sea interactions off the coast of Peru and Chile using the Scripps Coupled Ocean-Atmosphere Regional (SCOAR) model. We quantify and diagnose the effects of SST distribution on atmospheric stability and cloud variability, by comparing the SCOAR run with the uncoupled Regional Spectral Model (RSM). Likewise, we investigate the impact of wind forcing upon mixed layer depth and mesoscale eddy statistics by contrasting the SCOAR run and the uncoupled Regional Ocean Modeling System (ROMS) run.