Two distinct nocturnal subcanopy flow regimes are observed beneath a tall (16 m) open pine forest canopy. The first is characterized by weaker mixing, stronger stability, westerly downslope flow decoupled from the flow above the canopy and much smaller than expected ecosystem respiration from the eddy flux plus storage measurements compared to estimates based on chambers (missing carbon dioxide). The second regime is characterized by stronger mixing, weaker stability, southerly flow coupled to the flow above the canopy and good agreement between the eddy flux plus storage estimate and the chamber-based estimate of ecosystem respiration. The observations show that the inferred advection terms dominate the carbon dioxide budget in the first regime and are small relative to the eddy flux plus storage terms in the stronger mixing second regime, where the advection is estimated as a residual taking chamber-based measurements of respiration as truth. The friction velocity, standard deviation of vertical velocity, bulk Richardson number, Monin–Obukhov length scale and the subcanopy 3-m wind direction are all good indicators of missing carbon dioxide at this site.