The online-coupled Weather Research and Forecasting model with Chemistry (WRFchem) is used to simulate the transport of smoke particles over the Southeast Asian Maritime Continent during September–October 2006. In this period, dry conditions associated with the moderate El Niño event caused the largest regional biomass burning outbreak since 1997. Smoke emission in WRFchem is specified according to the Fire Locating and Modeling of Burning Emissions (FLAMBE) database derived from Moderate Resolution Imaging Spectroradiometer (MODIS) fire products. The modeled smoke transport pathway is found to be consistent with the MODIS true color images and measured mass concentration of surface PM10 (particulate matter with diameter less than 10 μm). The interplay of sea/land breezes, typhoons and storms over the subtropical western Pacific Ocean, trade winds, and topographic effects, can be clearly seen in the model simulation. The most severe smoke events in 1–5 October 2006 are found to be associated with the meteorological responses to the typhoon Xangsane (#18) over the western subtropical Pacific Ocean, which moved smoke from Sumatra eastward in the lower troposphere (below 700 hPa), forming smoke layers mixed with and above the boundary layer clouds over Borneo. In contrast, the second largest week-long smoke transport event of 15–18 October 2006 was associated with the seasonal monsoonal transition period, during which smoke plumes were wide spread over the 5°S–5°N zone as a result of (a) the near surface divergence coupled with the 700 hPa bifurcation of wind (flowing both to the west and to the east), and (b) the near-surface southeasterly and easterly winds along the equator transporting smoke from Borneo to Sumatra and Peninsular Malaysia. Analysis of data from the Cloud-Aerosol Lidar with Orthogonal Polarisation (CALIOP) shows that smoke particles in October 2006 were primarily located within 3.5 km above the surface. Smoke particles contributed roughly half of the total aerosol extinction retrieved by CALIOP. Results suggest that the smoke injection height in the model should be set lower than the 2–5 km commonly used in transport simulations; smoke release at ~ 0.8 km instead of 2 km above surface gives a consistently better match to CALIOP observations. Numerical experiments further show that the Titiwangsa Mountains in Malaysia Peninsula and Tama Abu Mountains in Borneo have significant impacts on smoke transport and the surface air quality in the vicinity.