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• Interplay of different flow regimes influences the Amazonian nocturnal boundary layer. • Strong stability in the Amazonia NBL allows the interaction of a gravity wave and LLJ. • During the inception of the gravity wave the turbulent fluxes are very small. • Confining the scalar below the LLJ nose at the forest-atmosphere interface. We investigated the role of turbulent coherent structures (CS), gravity waves (GW) and low-level jet (LLJ) propagation in the flow dynamics of the Nocturnal Boundary Layer (NBL) within and above a forest canopy at the Amazon Tall Tower Observatory (ATTO), in Central Amazon. Seven levels of wind velocity and temperature measurements allowed the study of the flow structure below and above the surface layer. We analyzed one dynamically rich night in 2015, which includes three distinct periods. In the first one, the NBL is characterized by CS generated at the canopy top. In the second period, the change in wind direction triggers the onset of a orographic GW above the roughness sublayer. The wave, suppressing the propagation of CS, strongly influences the boundary layer structure, both above and below the canopy. In the third period, low turbulence intensity at the canopy top enables the development of a LLJ. As the jet shear layer propagates upward, it disrupts the wave oscillations, while LLJ dominates the flow dynamics. The wavelet analyses identified i) turbulent and non-turbulent structures with different length and time-scales; ii) coupling of the flow at different levels and the vertical propagation of turbulent and wave motions; and iii) the ability of turbulent and low frequency processes associated with the orographic GW to penetrate within the canopy. Further, scalar measurements of methane, carbon monoxide and carbon dioxide identified the LLJ nose as upward limit for how far scalars can be transported. [ABSTRACT FROM AUTHOR]