To assess the effects of soil water status on the spatial variation in soil carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) fluxes, we examined these gas fluxes and environmental factors in a tropical rain forest in Peninsular Malaysia. Measurements of soil CO2, CH4 and N2O fluxes were taken ten, nine, and seven times, respectively over 30 mo at 15 or 39 sampling point within 2-ha plot. Mean (± SE) value of spatially averaged CO2 flux was 4.70 ± 0.19 μmol CO2 m−2 s−1 and observed spatial variation in CO2 flux was negatively related to the volumetric soil water content (VSWC) during the dry period. Over the wet period, extremely high CO2 emissions were positively correlated with VSWC at some locations, suggesting that no spatial structure of CO2 flux was because of such hot-spot CO2 emissions. Flux of CH4 was usually negative with little variation, with a mean value of –0.49 ± 0.15 mg CH4 m−2 d−1, resulting in the soil at our study site functioning as a CH4 sink. Spatial variation in CH4 flux was positively related to the VSWC throughout the entire study period (dry and wet). Some CH4 hot spots were observed during dry periods, probably due to the presence of termites. Mean value of spatially averaged N2O flux was 98.9 ± 40.7 μg N m−2 h−1 and N2O flux increased markedly during the wet period. Spatially, N2O flux was positively related to both the VSWC and the soil N concentration and was higher in wet and anaerobic soils. These findings suggest that denitrification is a major contributor to high soil N2O fluxes. Additionally, analysis by adjusting confounding effects of time, location and interaction between time and location in mixed models, VSWC has a negative effect on CO2 flux and positive effects on CH4 and N2O fluxes. We found that soil water status was related temporally to rainfall and controlled greenhouse gas (GHG) fluxes from the soil at the study site via several biogeochemical processes, including gas diffusion and soil redox conditions. Our results also suggest that considering the biological effects such as decomposer activities may help to explain the complex temporal and spatial patterns in CO2 and CH4 fluxes.