The magnitude and dynamics of soil gaseous fluxes play critical roles in the global gas balance; yet, these processes are not captured at sufficient temporal resolution by standard methods based on periodic sampling and surface chamber measurements. A novel method for continuous measurement of soil surface gas fluxes based on subsurface CO2 and O2 concentration gradient measurements was developed. We tested the gradient-based method under steady- and transient-state soil water content and temperature conditions and compared results with a state-of-the-art surface chamber CO2 flux system. The new aspects of the method include fast-response sensors installed in the soil profile providing continuous record of concentration gradients coupled with concurrent estimates of water content-dependent gaseous diffusion coefficient enabling calculation of surface gaseous fluxes. Low-cost infrared sensors were used for CO2 concentration measurements, and galvanic cells for O2 measurements. An imposed CO2 concentration gradient in a dry soil column resulted in a quasilinear CO2 concentration profile and surface CO2 flux in agreement with chamber-measured fluxes. A series of continuous concentration measurements under variable water content conditions and wetting events showed agreement with surface chamber measurements. Within several days of surface wetting, soil CO2 concentrations attained 10 mL L−1, one order of magnitude higher than ambient concentrations, whereas O2 concentrations decreased. The gradient-based approach minimizes soil surface perturbations and provides insights into subsurface soil CO2 and O2 dynamics and the distribution and magnitude of soil respiration processes as related to soil environmental factors. The subsurface gradient-based measurement system represents an order-of-magnitude reduction in cost compared with research-grade surface chamber devices.