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In this work, we study numerically with large eddy simulation, the effects induced by the three-dimensional geometry of the channel on the flow topology that exists when the three-dimensional intrinsic instabilities appear in a backward facing step flow with low aspect ratio for Reynolds in the transitional regime (Re = 1,000&-1,600), and its impact on the heat flux in the lower wall. Under the transitional regime, the three-dimensional instabilities begin to appear, but they can be masked by the flows due to the presence of the side walls. The study is carried out with two boundary conditions in the sidewalls, slip, and no-slip, to discriminate between the three-dimensionality induced by the geometry and the intrinsic three-dimensional instabilities. The results obtained are compared between the two boundary conditions, establishing what type of flow prevails and its influence on time-averaged mean Nusselt number for all Reynolds.