Low-level clouds in the Arctic affect the surface energy budget and vertical transport of heat and moisture. The limited availability of cloud-droplet-forming aerosol particles strongly impacts cloud properties and lifetime. Vertical particle distributions are required to study aerosol–cloud interaction over sea ice comprehensively. This article presents vertically resolved measurements of aerosol particle number concentrations and sizes using tethered balloons. The data were collected during the Multidisciplinary drifting Observatory for the Study of Arctic Climate expedition in the summer of 2020. Thirty-four profiles of aerosol particle number concentration were observed in 2 particle size ranges: 12–150 nm (N12−150) and above 150 nm (N>150). Concurrent balloon-borne meteorological measurements provided context for the continuous profiles through the cloudy atmospheric boundary layer. Radiosoundings, cloud remote sensing data, and 5-day back trajectories supplemented the analysis. The majority of aerosol profiles showed more particles above the lowest temperature inversion, on average, double the number concentration compared to below. Increased N12−150 up to 3,000 cm−3 were observed in the free troposphere above low-level clouds related to secondary particle formation. Long-range transport of pollution increased N>150 to 310 cm−3 in a warm, moist air mass. Droplet activation inside clouds caused reductions of N>150 by up to 100%, while the decrease in N12−150 was less than 50%. When low-level clouds were thermodynamically coupled with the surface, profiles showed 5 times higher values of N12−150 in the free troposphere than below the cloud-capping temperature inversion. Enhanced N12−150 and N>150 interacting with clouds were advected above the lowest inversion from beyond the sea ice edge when clouds were decoupled from the surface. Vertically discontinuous aerosol profiles below decoupled clouds suggest that particles emitted at the surface are not transported to clouds in these conditions. It is concluded that the cloud-surface coupling state and free tropospheric particle abundance are crucial when assessing the aerosol budget for Arctic low-level clouds over sea ice.