Agriculturally impacted ecosystems can be a source of the greenhouse gas, nitrous oxide (N(2)O); yet in situ measurements of N(2)O fluxes are sparse, particularly in streams and rivers. Dissolved N(2)O was measured from 9 sites over a 13-month period and a gas exchange model was used to predict N(2)O fluxes. N(2)O fluxes were measured at 4 sites on 7 sampling dates using floating chambers. In addition, dissolved N(2)O in porewaters was measured at 4 sites at various depths from 2 to 30 cm. Dissolved N(2)O-N concentrations in surface waters (0.31-1.60 μg L(-1)) varied seasonally with highest concentrations in late fall and early summer and lowest in winter. Estimated N(2)O-N fluxes (26.2-207 μg m(-2) hr(-1)) were in relative agreement with measured N(2)O fluxes using floating chambers (9.5-372 μg m(-2) hr(-1)) and correlated strongly with temperature and nitrate concentrations (R(2) = 0.86). Maximum dissolved N(2)O-N:NO(3)(-)-N ratios were higher in sediment-porewaters at 0.16, compared to surface waters (0.010). The calculated EF5-r value (mean = 0.0028; range = 0.0012-0.0069) was up to 3 times greater than the current IPCC EF5-r emissions factor (0.0025 kg N(2)O-N emitted per kg of NO(3)(-)-N leached). The highest EF5-r values were found in the high-flow sampling events when dissolved N(2)O and NO(3)(-) concentrations were low, highlighting potential constraints in the IPCC methodology for large rivers.