Abstract. To clarify the factors controlling temporal and spatial variations of soil carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) fluxes, we investigated these gas fluxes and environmental factors in a tropical rainforest in Peninsular Malaysia. Temporal variation of CO₂ flux in a 2-ha plot was positively related to soil water condition and rainfall history. Spatially, CO₂ flux was negatively related to soil water condition. When CO₂ flux hotspots were included, no other environmental factors such as soil C or N concentrations showed any significant correlation. Although the larger area sampled in the present study complicates explanations of spatial variation of CO₂ flux, our results support a previously reported bipolar relationship between the temporal and spatial patterns of CO₂ flux and soil water condition observed at the study site in a smaller study plot. Flux of CH₄ was usually negative with little variation, resulting in the soil at our study site functioning as a CH₄ sink. Both temporal and spatial variations of CH₄ flux were positively related to the soil water condition. Soil N concentration was also related to the spatial distribution of CH₄ flux. Some hotspots were observed, probably due to CH₄ production by termites, and these hotspots obscured the relationship between both temporal and spatial variations of CH₄ flux and environmental factors. Temporal variation of N₂O flux and soil N₂O concentration was large and significantly related to the soil water condition, or in a strict sense, to rainfall history. Thus, the rainfall pattern controlled wet season N₂O production in soil and its soil surface flux. Spatially, large N₂O emissions were detected in wet periods at wetter and anaerobic locations, and were thus determined by soil physical properties. Our results showed that, even in Southeast Asian rainforests where distinct dry and wet seasons do not exist, variation in the soil water condition related to rainfall history controlled the temporal variations of soil CO₂ flux, CH₄ uptake, and N₂O emission. The soil water condition associated with soil hydraulic properties was also the important controlling factor of the spatial distributions of these gas fluxes.