We evaluate a comprehensive soil CO2 survey along the San Andreas fault (SAF) in Parkfield, and the Calaveras fault (CF) in Hollister, California, in the context of spatial and temporal variability, origin, and transport of CO2 in fractured terrain. CO2 efflux was measured within grids with portable instrumentation and continuously with meteorological parameters at a fixed station, in both faulted and unfaulted areas. Spatial and temporal variability of surface CO2 effluxes was observed to be higher at faulted SAF and CF sites, relative to comparable background areas. However, δ13C (-23.3 to -16.4?) and Δ14C (75.5 to 94.4?) values of soil CO2 in both faulted and unfaulted areas are indicative of biogenic CO2, even though CO2 effluxes in faulted areas reached values as high as 428 g m-2 d-1. Profiles of soil CO2 concentration as a function of depth were measured at multiple sites within SAF and CF grids and repeatedly at two locations at the SAF grid. Many of these profiles suggest a surprisingly high component of advective CO2 flow. Spectral and correlation analysis of SAF CO2 efflux and meteorological parameter time series indicates that effects of wind speed variations on atmospheric air flow though fractures modulate surface efflux of biogenic CO2. The resulting areal patterns in CO2 effluxes could be erroneously attributed to a deep gas source in the absence of isotopic data, a problem that must be addressed in fault zone soil gas studies.