Sediment denitrification is an important nitrate (NO3-) removal process from agricultural streams. The direct and indirect factors that control denitrification rates in tributary sediments can vary depending on the types of agricultural activities and vegetation. Our research investigated (1) tributary sediment denitrification rates in a grassland stream affected by pasture ecosystems and a forest stream affected by N fertilization; and (2) the environmental factors that determine denitrification rates in tributary sediments. The denitrification enzyme activity (DEA) in grassland stream sediments is positively correlated with precipitation likely due to the increased nutrient exchange rates between stream water and sediments, and was higher than in forest stream sediments, leading to a decrease in NO3- concentration ([NO3-]) in stream sediments. The DEA in riparian sediments was regulated by carbon concentrations and did not contribute to NO3- removal from the riparian sediment in grassland and forest streams. Thus, environmental factors affected by different types of agricultural activities and vegetation might regulate denitrification rates and [NO3-] in agricultural stream ecosystems.