In this paper, we seek to understand the roles of three classes of physical processes in driving the cloud and water vapor distributions in the TTL: (1) various scales of temperature variation; (2) convective injection; and (3) microphysics. The approach is to use a comprehensive one-dimensional microphysical model in the context of trajectory simulations of the entire TTL for the 2006-2007 boreal winter. Results are compared with cloud and water vapor distributions from the A-train satellites. The findings from recent aircraft field campaigns are used in the microphysical model, while A-train measurements of convective cloud top heights are used in parameterizing convective injection. Not surprisingly, making appropriate corrections to the basic large scale temperature variations is the most important factor in the water vapor distribution. However, including microphysics, convection, and gravity waves each affect the TTL water vapor by about .5 ppmv. Overall, including all processes enhances water vapor by about .5 ppmv over simple removal at ice saturation.