AbstractWe evaluate local differences in thermal regimes and turbulent heat fluxes across the heterogeneous canopy of a black spruce boreal forest on discontinuous permafrost in interior Alaska. The data were taken during an intensive observing period in the summer of 2013 from two micrometeorological towers 600 m apart in a central section of boreal forest, one in a denser canopy (DC) and the other in a sparser canopy, but under approximately similar atmospheric boundary layer (ABL) flow conditions. Results suggest that on average 34% of the half‐hourly periods in a day are nonstationary, primarily during night and during ABL transitions. Also, thermal regimes differ between the two towers; specifically between midnight and 0500 Alaska Standard Time (AKST) it is about 3°C warmer at DC. On average, the sensible heat flux at DC was greater. For midday periods, the difference between those fluxes exceeded 30% of the measured flux and over 30 W m−2 in magnitude more than 60% of the time. These differences are due to higher mechanical mixing as a result of the increased density of roughness elements at DC. Finally, the vertical distribution of turbulent heat fluxes verifies a maximum atop the canopy crown (2.6 h) when compared with the subcanopy (0.6 h) and above canopy (5.1 h), where h is the mean canopy height. We argue that these spatial and vertical variations of sensible heat fluxes result from the complex scale aggregation of energy fluxes over a heterogeneous canopy.