Rapid increases in nitrogen (N) loading are occurring in many tropical watersheds, but the fate of N in tropical streams is not well documented. Rates of nitrate uptake and denitrification were measured in nine tropical low-order streams with contrasting land use as part of the Lotic Intersite Nitrogen eXperiment II (LINX II) in Puerto Rico using short term (24-hour) additions of K15NO3 and NaBr. Background nitrate concentrations ranged from 105 to 997 μg N/L, and stream nitrate uptake lengths were long, varying from 315 to 8480 m (median of 1200 m). Other indices of nitrate uptake (mass transfer coefficient, Vf [cm/s], and whole-stream nitrate uptake rate, U [μg N·m−2·s−1]) were low in comparison to other regions and were related to chemical, biological, and physical parameters. Denitrification rates were highly variable (0–133 μg N·m−2·min−1; median = 15 μg N·m−2·min−1), were dominated by the end product N2 (rather than N2O), and were best predicted by whole-stream respiration rates and stream NO3 concentration. Denitrification accounted for 1–97% of nitrate uptake with five of nine streams having 35% or more of nitrate uptake via denitrification, showing that denitrification is a substantial sink for nitrate in tropical streams. Whole-stream nitrate uptake and denitrification in our study streams closely followed first-order uptake kinetics, indicating that NO3 uptake is limited by delivery of substrate (NO3) to the organisms involved in uptake or denitrification. In the context of whole-catchment nitrogen budgets, our finding that in-stream denitrification results in lower proportional production of N2O than terrestrial denitrification suggests that small streams can be viewed as the preferred site of denitrification in a watershed in order to minimize greenhouse gas N2O emissions. Conservation of small streams is thus critical in tropical ecosystem management.