Microsensors, including a recently developed NO₃ biosensor, were applied to measure O₂ and NO₃ profiles in marine sediments from the upwelling area off central Chile and to investigate the influence of Thioploca spp. on the sedimentary nitrogen metabolism. The studies were performed in undisturbed sediment cores incubated in a small laboratory flume to simulate the environmental conditions of low O₂, high NO₃, and bottom water current. On addition of NO₃ and NO₂, Thioploca spp. exhibited positive chemotaxis and stretched out of the sediment into the flume water. In a core densely populated with Thioploca, the penetration depth of NO₃ was only 0.5 mm and a sharp maximum of NO₃ uptake was observed 0.5 mm above the sediment surface. In sediments with only few Thioploca spp., NO₃ was detectable down to a depth of 2 mm and the maximum consumption rates were observed within the sediment. No chemotaxis toward nitrous oxide (N₂O) was observed, which is consistent with the observation that Thioploca does not denitrify but reduces intracellular NO₃ to NH₄⁺. Measurements of the intracellular NO₃ and S⁰ pools in Thioploca filaments from various depths in the sediment gave insights into possible differences in the migration behavior between the different species. Living filaments containing significant amounts of intracellular NO₃ were found to a depth of at least 13 cm, providing final proof for the vertical shuttling of Thioploca spp. and nitrate transport into the sediment.