The higher-order scalar concentration fluctuation properties are examined in the context of Monin–Obukhov similarity theory for a variety of greenhouse gases that have distinct and separate source/sink locations along an otherwise ideal micrometeorological field site. Air temperature and concentrations of water vapour, carbon dioxide and methane were measured at high frequency (10 Hz) above a flat and extensive peat-land soil in the San Joaquin–Sacramento Delta (California, USA) area, subjected to year-round grazing by beef cattle. Because of the heterogeneous distribution of the sources and sinks of CO2 and especially CH4emitted by cattle, the scaling behaviour of the higher-order statistical properties diverged from predictions based on a balance between their production and dissipation rate terms, which can obtained for temperature and H2O during stationary conditions. We identify and label these departures as ‘exogenous’ because they depend on heterogeneities and non-stationarities induced by boundary conditions on the flow. Spectral analysis revealed that the exogenous effects show their signatures in regions with frequencies lower than those associated with scalar vertical transport by turbulence, though the two regions may partially overlap in some cases. Cospectra of vertical fluxes appear less influenced by these exogenous effects because of the modulating role of the vertical velocity at low frequencies. Finally, under certain conditions, the presence of such exogenous factors in higher-order scalar fluctuation statistics may be ‘fingerprinted’ by a large storage term in the mean scalar budget.