In a joint NRL/Manila Observatory mission, as part of the Seven SouthEast Asian Studies program (7-SEAS), a 2-week, late September 2011 research cruise in the northern Palawan archipelago was undertaken to observe the nature of southwest monsoonal aerosol particles in the South China Sea/East Sea (SCS/ES) and Sulu Sea region. Previous analyses suggested this region as a receptor for biomass burning from Borneo and Sumatra for boundary layer air entering the monsoonal trough. Anthropogenic pollution and biofuel emissions are also ubiquitous, as is heavy shipping traffic. Here, we provide an overview of the regional environment during the cruise, a time series of key aerosol and meteorological parameters, and their interrelationships. Overall, this cruise provides a narrative of the processes that control regional aerosol loadings and their possible feedbacks with clouds and precipitation. While 2011 was a moderate El Niño–Southern Oscillation (ENSO) La Niña year, higher burning activity and lower precipitation was more typical of neutral conditions. The large-scale aerosol environment was modulated by the Madden–Julian Oscillation (MJO) and its associated tropical cyclone (TC) activity in a manner consistent with the conceptual analysis performed by Reid et al. (2012). Advancement of the MJO from phase 3 to 6 with accompanying cyclogenesis during the cruise period strengthened flow patterns in the SCS/ES that modulated aerosol life cycle. TC inflow arms of significant convection sometimes span from Sumatra to Luzon, resulting in very low particle concentrations (minimum condensation nuclei CN < 150 cm−3, non-sea-salt PM2.5 < 1 μg m−3). However, elevated carbon monoxide levels were occasionally observed suggesting passage of polluted air masses whose aerosol particles had been rained out. Conversely, two drier periods occurred with higher aerosol particle concentrations originating from Borneo and Southern Sumatra (CN > 3000 cm−3 and non-sea-salt PM2.5 10–25 μg m−3). These cases corresponded with two different mechanisms of convection suppression: lower free-tropospheric dry-air intrusion from the Indian Ocean, and large-scale TC-induced subsidence. Veering vertical wind shear also resulted in aerosol transport into this region being mainly in the marine boundary layer (MBL), although lower free troposphere transport was possible on the western sides of Sumatra and Borneo. At the hourly time scale, particle concentrations were observed to be modulated by integer factors through convection and associated cold pools. Geostationary satellite observations suggest that convection often takes the form of squall lines, which are bowed up to 500 km across the monsoonal flow and 50 km wide. These squall lines, initiated by cold pools from large thunderstorms and likely sustained by a veering vertical wind shear and aforementioned mid-troposphere dry layers, propagated over 1500 km across the entirety of the SCS/ES, effectively cutting large swaths of MBL aerosol particles out of the region. Our conclusion is that while large-scale flow patterns are very important in modulating convection, and hence in allowing long-range transport of smoke and pollution, more short-lived phenomena can modulate cloud condensation nuclei (CCN) concentrations in the region, resulting in pockets of clean and polluted MBL air. This will no doubt complicate large scale comparisons of aerosol–cloud interaction.