When highly reactive chain transfer agents with low water solubilities (e.g., long chain thiols) are used in emulsion polymerizations, transport of the chain transfer agent (CTA) from the monomer droplets to the polymer particles can become diffusion limited. Consequently, the concentration of CTA in the particles is lower than expected, resulting in apparent transfer constants that can be much lower than the actual transfer constants obtained from studies with homogeneous systems such as bulk or solution. Furthermore, molecular weights will be greater than those obtained in homogeneous systems with the same overall concentration of CTA. There are currently no techniques or methodologies available for predicting molecular weight distributions when the transport of CTA is diffusion limited. Apparent transfer constants may be used but they are typically restricted to a given system and operating conditions. In this work, we describe how the actual CTA concentration in the polymer particles can be estimated through analysis of instantaneous molecular weight distributions. This information is then used to calculate the cumulative molecular weight distribution during the polymerization. Comparisons with experimental molecular weight distributions validate the essential correctness of the approach, but also highlight potential problems. The extension of the approach to online applications is discussed.