The effects of bioturbation in marine sediments are mainly associated with an increase in oxic and oxidized zones through an influx of oxygen-rich water deeper into the sediment and the rapid transport of particles between oxic and anoxic conditions. However, macrofaunal activity also can increase the occurrence of reduced microniches and anaerobic processes, such as sulfate reduction. Our goal was to determine the two-dimensional distribution of microniches associated with burrows of a ghost shrimp (Neotrypaea californiensis) and to determine microbial activities. In laboratory experiments, detailed measurements of sulfate reduction rates (SRR) were measured by injecting, in a 1 cm grid, radiolabelled sulfate directly into a narrow aquarium (40 cm × 30 cm × 3 cm) containing the complex burrow of an actively burrowing shrimp. Light-coloured oxidized burrow walls, along with black reduced microniches, were clearly visible through the aquarium walls. Direct injection of radiotracers allowed for whole-aquarium incubation to obtain two-dimensional documentation of sulfate reduction. Results indicated SRR were up to three orders of magnitude higher (140–790 nmol SO42− cm−3 day−1) in reduced microniches associated with burrows when compared with the surrounding sediment. Additionally, some of the subsurface sulfate-reducing microniches associated with the burrow system appeared to be zones of dinitrogen fixation. Bioturbation may also lead to decreased sulfate reduction in other microniches and the sum of the activity in all microniches might not result in a total increase of sulfate reduction compared with non-bioturbated control sediments.