Large uncertainties persist in estimates of soil–atmosphere exchange of important trace gases. One significant source of uncertainty is the combined effect of wind and pressure on these fluxes. Wind and pressure effects are mediated by surface topography: few surfaces are uniform and over scales of tenths of a metre to tens of metres, air pressure and wind speed at the ground surface may be very variable. In this paper we consider how such spatial variability in air pressure and wind speed affects fluxes of trace gases. We used a novel nested wind tunnel design comprising a toroidial wind tunnel, in which wind speed and pressure may be controlled, set within a larger, linear wind tunnel. The effects of both wind speed and pressure differentials on fluxes of CO2 and CH4 within three different ecosystems (forest, grassland, peat bog) were quantified. We find that trace gas fluxes are positively correlated with both wind speed and pressure differential near the surface boundary. We argue that wind speed is the better proxy for trace gas fluxes because of its stronger correlation and because wind speed is more easily measured and wind speed measurement methodology more easily standardized. Trace gas fluxes, whether into or out of the soil, increase with wind speed within the toroidal tunnel (+55 % flux per m s−1), while faster, localized surface winds that are external to the toroidal wind tunnel reduce trace gas fluxes (−13 % flux per m s−1). These results are consistent for both trace gases over all ecosystem soil types studied. Our findings support the need for a revised conceptualization of soil–atmosphere gas exchange. We propose a conceptual model of the soil profile that has a "mixed layer", with fluxes controlled by wind speed, wind duration, porosity, water table, and gas production and consumption.