Abstract. We use a nested version of the GEOS-Chem global 3-D chemistry transport model to better understand the composition and variation of aerosol over Borneo and the broader Southeast Asian region in conjunction with aircraft and satellite observations. Our focus on Southeast Asia reflects the importance of this region as a source of reactive organic gases and aerosols from natural forests, biomass burning, and food and fuel crops. We particularly focus on July 2008 when the UK BAe-146 research aircraft was deployed over northern Malaysian Borneo as part of the ACES/OP3 measurement campaign. During July 2008 we find using the model that Borneo (defined as Borneo Island and the surrounding Indonesian islands) was a net exporter of primary organic aerosol (42 kT) and black carbon aerosol (11 kT). We find only 13% of volatile organic compound oxidation products partition to secondary organic aerosol (SOA), with Borneo being a net exporter of SOA (15 kT). SOA represents approximately 19% of the total organic aerosol over the region. Sulphate is mainly from aqueous-phase oxidation (68%), with smaller contributions from gas-phase oxidation (15%) and advection into the regions (14%). We find that there is a large source of sea salt, as expected, but this largely deposits within the region; we find that dust aerosol plays only a relatively small role in the aerosol burden. In contrast to coincident surface measurements over Northern Borneo that find a pristine environment with evidence for substantial biogenic SOA formation we find that the free troposphere is influenced by biomass burning aerosol transported from the northwest of the Island and further afield. We find several transport events during July 2008 over Borneo associated with elevated aerosol concentrations, none of which coincide with the aircraft flights. We use MODIS aerosol optical depths (AOD) data and the model to put the July campaign into a longer temporal perspective. We find that Borneo is where the model has the least skill at reproducing the data, where the model has a negative bias of 76% and only captures 14% of the observed variability. This model performance reflects the small-scale island-marine environment and the mix of aerosol species, with the model showing more skill at reproducing observed AOD over larger continental regions such as China where AOD is dominated by one aerosol type. The model shows that AOD over Borneo is approximately evenly split between organic and sulphate aerosol with sea salt representing 10–20% during May–September; we find a similar breakdown over continental Southeast Asia but with less sea salt aerosol and more dust aerosol. In contrast, East China AOD is determined mainly by sulphate aerosol and a seasonal source of dust aerosol, as expected. Realistic sensitivity runs, designed to test our underlying assumptions about emissions and chemistry over Borneo, show that model AOD is most sensitive to isoprene emissions and organic gas-phase partitioning but all fail to improve significantly upon the control model calculation. This emphasises the multi-faceted dimension of the problem and the need for concurrent and coordinated development of BVOC emissions, and BVOC chemistry and organic aerosol formation mechanisms.