We employed a three-dimensional finite difference gas diffusion model to simulate the performance of chambers used to measure surface-atmosphere trace gas exchange. We found that systematic errors often result from conventional chamber design and deployment protocols, as well as key assumptions behind the estimation of trace gas exchange rates from observed concentration data. Specifically, our simulations showed that (1) when a chamber significantly alters atmospheric mixing processes operating near the soil surface, it also nearly instantaneously enhances or suppresses the postdeployment gas exchange rate, (2) any change resulting in greater soil gas diffusivity, or greater partitioning of the diffusing gas to solid or liquid soil fractions, increases the potential for chamber-induced measurement error, and (3) all such errors are independent of the magnitude, kinetics, and/or distribution of trace gas sources, but greater for trace gas sinks with the same initial absolute flux. Finally, and most importantly, we found that our results apply to steady state as well as non-steady-state chambers, because the slow rate of gas diffusion in soil inhibits recovery of the former from their initial non-steady-state condition. Over a range of representative conditions, the error in steady state chamber estimates of the trace gas flux varied from -30 to +32%, while estimates computed by linear regression from non-steady-state chamber concentrations were 2 to 31% too small. Although such errors are relatively small in comparison to the temporal and spatial variability characteristic of trace gas exchange, they bias the summary statistics for each experiment as well as larger scale trace gas flux estimates based on them. ¿ 2000 American Geophysical Union