The spatial variability of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) fluxes from forest soil with high nitrogen (N) deposition was investigated at a rolling hill region in Japan. Gas fluxes were measured on July 25th and December 5th, 2008 at 100 points within a 100 × 100 m grid. Slope direction and position influenced soil characteristics and site-specific emissions were found. The CO2 flux showed no topological difference in July, but was significantly lower in December for north-slope with coniferous trees. Spatial dependency of CH4 fluxes was stronger than that of CO2 or N2O and showed a significantly higher uptake in hill top, and emissions in the valley indicating strong influence of water status. N2O fluxes showed no spatial dependency and exhibited high hot spots at different topology in July and December. The high N deposition led to high N2O fluxes and emphasized the spatial variability.