Although nitrous oxide (N2O) emission from agricultural runoff is thought to constitute a globally important source of this greenhouse gas, N2O flux from polluted aquatic systems is poorly understood and scarcely reported, especially in low-latitude (0¿--30¿) regions where rapid agricultural intensification is occurring. We measured N2O emissions, dissolved N2O concentrations, and factors likely to control rates of N2O production in drainage canals receiving agricultural and mixed agricultural/urban inputs from the intensively farmed Yaqui Valley of Sonora, Mexico. Average per-area N2O flux in both purely agricultural and mixed urban/agricultural drainage systems (16.5 ng N2O-N cm-2 hr-1) was high compared to other fresh water fluxes, and extreme values ranged up to 244.6 ng N2O-N cm-2 hr-1. These extremely high N2O fluxes occurred during green algae blooms, when organic carbon, nitrogen, and oxygen concentrations were high, and only in canals receiving pig-farm and urban inputs, suggesting an important link between land-use and N2O emissions. N2O concentrations and fluxes correlated significantly with water column concentrations of nitrate, particulate organic carbon and nitrogen, ammonium, and chlorophyll a, and a multiple linear regression model including ammonium, dissolved organic carbon, and particulate organic carbon was the best predictor of 2O> (r2 = 52%). Despite high per-area N2O fluxes, our estimate of regional N2O emission from surface drainage (20,869 kg N2O-N yr-1; 0.046% of N-fertilizer inputs) was low compared to values predicted by algorithms used in global budgets.