The cloud condensation nuclei (CCN) concentrations greatly determine the vertical microphysical evolution and rain initiation of warm convective clouds. We investigated the vertical profile of aerosol particles large enough (diameter > 60 nm) to act as CCN in marine air masses over the Great Barrier Reef. Such data were collected during an aircraft research campaign in February 2024. The results show a strong relationship between the microphysical processes measured in the cloud and the aerosol properties measured at the same altitude. The number concentration of aerosol particles decreases significantly above cloud bases due to CCN activation into cloud droplets. For heights above the in-cloud rain initiation level, the aerosol concentrations decrease further due to the scavenging of particles by drizzle and raindrops. The Hoppel minimum in particle size distributions is observed up to the altitude at which the coagulation process intensifies. Furthermore, a tail of larger aerosol particles was measured above the altitudes of rain initiation. These results suggest that the vertical profile of aerosols measured in marine air masses is dominated by cloud processing. Plain text summary: Understanding the role of aerosol-cloud interactions is crucial information in accurately predicting the effects of climate change on the Great Barrier Reef (GBR). Characterizing the properties of aerosol particles found over the Reef is essential in determining their ability to act as cloud condensation nuclei (CCN). The evaporation of cloud droplets and raindrops represents an additional source that may influence the concentrations and sizes of aerosol. Here, we show that warm clouds dominate the vertical profiles of aerosol particles in the lower troposphere over the GBR. Our research shows that marine clouds work like a sink of aerosol particles found over the Reef. The cloud microphysical processes (activation of CCN into cloud droplets and the collision and coalescence processes) decrease the concentration of aerosol particles at the same altitude in the lower troposphere. Cloud processing develops the “Hoppel minima” or Hoppel minimum of the marine boundary layer aerosol size distributions as clouds evaporate. The Hoppel minimum is not observed in the particle size distributions above altitudes of intense coagulation processes. Above this level, the ultrafine particles dominate the aerosol concentrations.