Denitrification within riparian buffers may trade reduced nonpoint source pollution of surface waters for increased greenhouse gas emissions resulting from denitrification-produced nitrous oxide (N2O). However, little is known about the N2O emission within conservation buffers established for water quality improvement or of the importance of short-term N2O peak emission following rewetting dry soils and thawing frozen soils. Such estimates are important in reducing uncertainties in current Intergovernmental Panel on Climate Change (IPCC) methodologies estimating soil N2O emission which are based on N inputs. This study contrasts N2O emission from riparian buffer systems of three perennial vegetation types and an adjacent crop field, and compares measured N2O emission with estimates based on the IPCC methodology. We measured soil properties, N inputs, weather conditions and N2O fluxes from soils in forested riparian buffers, warm-season and cool-season grass filters, and a crop field located in the Bear Creek watershed in central Iowa, USA. Cumulative N2O emissions from soils in all riparian buffers (5.8 kg N2O-N ha−1 in 2006–2007) were significantly less than those from crop field soils (24.0 kg N2O-N ha−1 in 2006–2007), with no difference among the buffer vegetation types. While N2O peak emissions (up to 70-fold increase) following the rewetting of dry soils and thawing of frozen soils comprised 46–70% of the annual N2O emissions from soils in the crop field, soils in the riparian buffers were less sensitive to such events (3 to 10-fold increase). The ratio of N2O emission to N inputs within riparian buffers (0.02) was smaller than those of crop field (0.07). These results indicate that N2O emission from soils within the riparian buffers established for water quality improvement should not be considered a major source of N2O emission compared to crop field emission. The observed large difference between measured N2O emissions and those estimated using the IPCC's recommended methodology (i.e., 87% underestimation) in the crop field suggests that the IPCC methodology may underestimate N2O emission in the regions where soil rewetting and thawing are common, and that conditions predicted by future climate-change scenarios may increase N2O emissions.