Sediment diversions along the lower Mississippi River have been proposed to help slow the rate of wetland loss in Louisiana by transferring sediment from the river to coastal marshes, facilitating wetland accretion. While diversions will provide relief to sediment starved coastal wetlands, they will also deliver significant amounts of nutrients (primarily N as NO3–) to receiving basins with potential for negative water quality impacts. There is a paucity of data on nitrate removal rates in the “near-field” area of diversions, identified as areas in immediate proximity to diversion outfalls. In these environments, well-mixed turbulent water column conditions can impart significant shear stress on the sediment surface, suspending fine grained sediments. It is critical to determine nitrate reduction in this near-field environment to predict the potential impact of N on the receiving basins of sediment diversions. Sediment cores were collected from three sites within a mudflat in an active deltaic setting in coastal Louisiana, representative of sediment in the receiving basins, and subjected to shear stress using a flow-through erosional microcosm system for 24 h. Nitrate reduction rates were 18.7 ± 20.2, 186 ± 55.1 and 303 ± 65.6 mg N m−2 d−1 determined under zero, medium and high shear stress conditions of 0, 0.2, and 0.45 Pa, respectively. Nitrate reduction rates were ∼10–16 times faster as shear stress increased. These results indicate that even under well-oxygenated, turbulent flow water column conditions, nitrate can be significantly reduced through the reworking and resuspension of sediment. This research can help inform diversion models and assist natural resource managers in predicting potential nutrient loads and associated impacts of river diversions on shallow estuarine receiving basins as well as being applicable to other flowing systems.