The application of Monin–Obukhov similarity theory (MOS) is based on empirical relationships derived over uniform surfaces in flat terrain. It is not clear to what extent these relationships hold for complex surfaces such as tropical forest or hilly terrain. This study investigates the influence of low-frequency motions in the structure of the atmospheric surface layer over Amazonian forest and its implication for the application of MOS theory. We test the estimation of heat fluxes by the flux-variance method, which is based on MOS theory, for measurements in unstable conditions in the K34 forest site in central Amazonia, north of Manaus, Brazil. It is found that the MOS relationships and the flux-variance method provide reasonable results only when the w−T correlation (rwT) is above 0.5. Examining the scale dependence of rwT and of u−w correlation (ruw) revealed that w variations tend to be not well correlated with fluctuations in u or T at low frequencies. In this sense, a greater influence of low-frequency processes tends to cause rwT and ruw to decrease, and in these conditions the surface layer cannot be characterized by the ‘textbook’ descriptions of the surface layer observed over uniform terrain. As an alternative to the conventional MOS scaling, we test the use of the ‘dissipation velocity’ uɛ = (kzɛ)1/3, proposed by McNaughton [McNaughton, K.G., 2006. On the kinetic energy budget of the unstable atmospheric surface layer. Boundary-Layer Meteorol. 118, 83–107], to scale the standard deviations and parameterize the modulation of low-frequency motions. The systematic variation with stability is taken out by the use of the new parameters, and the scaled variables become independent of the MOS stability parameter ζ. This result is consistent with the self-organizing nature of the turbulent structure in the modulated surface layer. The results highlight the complexities of the surface layer above vegetation such as Amazonian forest. Estimations of the parameter υ*/u*, which represent the modulation of the outer-layer motions on the surface layer, indicate that during roughly 20% of the time the unstable surface layer above the forest deviates from the ‘classical’ description.