A convection-permitting limited area model with periodic lateral boundary conditions and prognostic aerosol microphysics is applied to investigate how concentrations of cloud condensation nuclei (CCN) in the marine boundary layer are affected by high-resolution dynamical and thermo-dynamic fields. The high-resolution aerosol microphysics-dynamics model, which resolves differential particle growth and aerosol composition across the particle size range, is applied to a domain designed to match approximately a single grid square of a climate model. We find that, during strongly convective conditions with high wind-speed conditions, CCN concentrations vary by more than a factor of 8 across the domain (5-95th percentile range), and a factor of ∼ 3 at more moderate wind speed. One reason for these large sub-climate-grid-scale variations in CCN is that emissions of sea salt and dimethyl sulfide (DMS) are much higher when spatial and temporal wind-speed fluctuations become resolved at this convection-permitting resolution (making peak wind speeds higher). By analysing how the model evolves during spin-up, we gain new insight into the way primary sea salt and secondary sulfate particles contribute to the overall CCN variance in these realistic conditions, and find a marked difference in the variability of super-micron and sub-micron CCN. Whereas the super-micron CCN are highly variable, dominated by strongly fluctuating sea spray emitted, the sub-micron CCN tend to be steadier, mainly produced on longer timescales following growth after new particle formation in the free troposphere, with fluctuations inherently buffered by the fact that coagulation is faster at higher particle concentrations. We also find that sub-micron CCN are less variable in particle size, the accumulation-mode mean size varying by ∼ 20 % (0.101 to 0.123 µm diameter) compared to ∼ 35 % (0.75 to 1.10 µm diameter) for coarse-mode particles at this resolution. We explore how the CCN variability changes in the vertical and at different points in the spin-up, showing how CCN concentrations are introduced both by the emissions close to the surface and at higher altitudes during strong wind-speed conditions associated to the intense convective period. We also explore how the non-linear variation of sea-salt emissions with wind speed propagates into variations in sea-salt mass mixing ratio and CCN concentrations, finding less variation in the latter two quantities due to the longer transport timescales inherent with finer CCN, which sediment more slowly. The complex mix of sources and diverse community of processes involved makes sub-grid parameter-isation of CCN variations difficult. However, the results presented here illustrate the limitations of predictions with large-scale models and the high-resolution aerosol microphysics-dynamics modelling system shows promise for future studies where the aerosol variations will propagate through to modified cloud microphysical evolution.