A trajectory ensemble model (TEM) is used to investigate aqueous processing of gases and cloud condensation nuclei (CCN) in the boundary layer. The coupled aqueous chemistry/cloud microphysics model driven by a set of boundary layer parcel trajectories derived from a large eddy simulation is used to study the effects of variations in the initial chemical fields and initial aerosol number concentration on chemical heterogeneity, and the broadening of CCN and drop spectra. The differences in the overall fractional conversion between the TEM and a single parcel experiencing mean conditions in a stratocumulus‐capped marine boundary layer are also investigated. Results show that the O3 oxidation rate is larger than the H2O2 oxidation rate in the base case, whereas the volume‐mean pH might suggest that H2O2 oxidation dominates. Aqueous chemistry contributes to broadening of the drop size distribution, but the magnitude of the broadening also depends on initial chemical conditions. Sensitivity tests show that the H2O2 oxidation adds sulfate mass evenly and continuously across the particle sizes, while the O3 oxidation adds sulfate mass near the mode of the CCN spectrum over a relatively short time. In cases where more mass is added onto large particles in the tail of the initial CCN spectrum, the broadening of the drop spectrum is most evident, and may even trigger the collision‐coalescence process and drizzle formation in stratocumulus clouds.