A three-dimensional groundwater flow and multispecies reactive transport model was used to strategically design placement of bioreactors in the subsurface to achieve maximum removal of nitrate along restored stream reaches. Two hypothetical stream restoration scenarios were evaluated over stream reaches of 40 and 94 m: a step-pool scenario and a channel re-meandering scenario. For the step-pool scenario, bioreactors were placed at locations where mass fluxes of groundwater and nitrate were highest. Bioreactors installed over 50% of the total channel length of a step-pool scenario (located to intercept maximum groundwater and nitrate mass flux) removed nitrate-N entering the channel at a rate of 36.5 kg N yr (100 g N d), achieving about 65% of the removal of a whole-length bioreactor. Bioreactor placement for the re-meandering scenario was designed using a criterion of either highest nitrate mass flux or highest groundwater flux, but not both, because they did not occur together. Bioreactors installed at maximum nitrate flux locations (53% of the total channel length) on the western bank removed nitrate-N entering the channel at 62.0 kg N yr (170 g N d), achieving 85% of nitrate-N removal of whole-length bioreactors for the re-meandering scenario. Bioreactors installed at maximum groundwater flux locations on the western bank along approximately 40% of the re-meandering channel achieved about 65% of nitrate removal of whole-length bioreactors. Placing bioreactors at maximum nitrate flux locations improved denitrification efficiency. Due to low groundwater velocities, bioreactor nitrate-N removal was found to be nitrate limited for all scenarios.