<p>The analysis of observed atmospheric trace gas mole fractions to infer surface sources and sinks of chemical species relies heavily on simulated atmospheric transport. The chemical transport models (CTMs) used in flux inversion models are commonly configured to reproduce the atmospheric transport of a general circulation model (GCM) as closely as possible. CTMs generally have the dual advantages of computational efficiency and improved tracer conservation compared to their parent GCMs, but they usually simplify the representations of important processes. This is especially the case for high-frequency vertical motions associated with diffusion and convection. Using common-flux experiments, we quantify the importance of parameterized vertical processes for explaining systematic differences in tracer transport between two commonly-used CTMs. We find that differences in convection are strongly correlated with the differences in modeled column CO<sub>2</sub>. The parameterization of diffusion is more important near the surface due to its role in representing PBL mixing. Accordingly, near-surface <em>in situ</em> measurements are more strongly impacted by this process than are total-column retrievals. Both diffusive and convective vertical mixing tend to ventilate the lower atmosphere, so near-surface measurements may only constrain the net vertical mixing and not the balance between these two processes. Remote sensing-based retrievals of total column CO<sub>2</sub>, with their increased sensitivity to convection, may provide important new constraints on parameterized vertical motions.</p>