AbstractPeriodic summer hypoxia occurring in the Northern Gulf of Mexico has been attributed to large nutrient inputs, especially nitrate‐nitrogen, from the Mississippi–Atchafalaya River system. The 2008 Gulf Hypoxia Action Plan calls for river corridor wetland restoration to reduce nitrate loads, but it is largely unknown how effective riverine wetland systems in the lower Mississippi River are for nitrate removal. We carried out an intensive isotope study to address this question by comparing nitrate isotopic signatures of the well‐channelized Mississippi River with those of the Atchafalaya River, which has extensive floodplains and backwater swamps. We investigated changes in δ15NNO3 and δ18ONO3 for water samples collected biweekly to monthly over a 2‐year period at the Atchafalaya River outlets (Morgan City and Wax Lake) and on the Mississippi River at Baton Rouge. In addition, in situ water quality parameters including temperature, dissolved oxygen and pH were recorded for each sampling date. Waters from both rivers showed moderately high nitrate concentration (>1 mg l−1) and undetectable (< 0.01 mg l−1) nitrite throughout the study period. The Mississippi River had slightly, but significantly higher (p=0.01) mean nitrate concentrations (1.5 mg l−1) and higher δ15NNO3 (7.7‰) than the Atchafalaya (1.1 mg l−1, 7.0‰); while no difference in δ18ONO3 (4.6‰) was found between the rivers. Flux‐weighted mean isotope values were overall lower than mean values for both the Mississippi and Atchafalaya Rivers, with a greater difference between the two rivers (7.4‰ versus 6.5‰, respectively). River flooding and hurricane storm surge also appeared to affect nitrate isotopic values. The lack of large difference in isotopic values between the Atchafalaya and Mississippi Rivers suggests that the majority of nitrate is transported through the Atchafalaya River with relatively little processing, and that riverine floodplains and wetlands are not effective sinks for nitrate, as previously assumed, because of insufficient residence time and well‐oxygenated river waters. Copyright © 2012 John Wiley & Sons, Ltd.