Squall lines (SLs) are convective systems that cause heavy precipitation and consequently modify the atmospheric thermodynamic structure near the surface. SLs generated along the northern coast of Brazil and their effect upon atmospheric structure during their westward displacement into the Amazon are studied. Satellite imagery was employed to identify an SL above two experimental sites in the central Amazon and to characterize differences in the near-surface turbulent and ozone exchange during the passage of the SLs. The two sites, which are separated by about 100 km, feature contrasting vegetation. One site is tall canopy rainforest and the other is deforested. From our case study, it is noted that: equivalent potential temperature significantly drops, principally in the forested region; the average near-surface wind speed increases 5 fold; the skewness of vertical wind velocity becomes considerably negative; significant increases in turbulence intensity are observed. These changes suggest the presence of strong downdrafts generated by the SL. Shear production and dissipation rate of turbulent kinetic energy are considerably larger during the SL when compared to periods with absence of SL. In this study, we show that SLs are capable of modifying the vertical organization of the turbulence over forested and deforested areas, leading to changes in certain chemical processes that occur near the surface. To the best of our knowledge, this study represents a first in demonstrating that near-surface turbulent flow in the Amazon region is modified by the presence of SLs.