The effect of sediment-dwelling macrofauna on nitrifying bacteria was investigated by direct probing in their overlapping habitat, i.e., the upper few millimeters of freshwater sediments. Microsensors (O 2 , NH þ 4 , NO 2 3 , and diffusivity) were used at the sediment surface and inside animal burrows to record steady-state and dynamic distributions of reactants, respectively. Short-term changes of metabolic activity (actual and potential nitrification rates) and long-term changes of abundance (fluorescence in situ hybridization) of nitrifying bacteria were determined. The presence of insect larvae (Chironomus riparius) increased the availability of O 2 and NO 2 3 in the sediment pore water and inside animal burrows, suggesting promotion of nitrification and dissimilatory NO 2 3 reduction, particularly in the burrowing layer of C. riparius. At the sediment surface (i.e., in the feeding layer of C. riparius), however, nitrification was inhibited by low NH þ 4 availability and high macrofaunal grazing pressure. Consequently, both actual and potential nitrification rates decreased in the feeding layer. Inside burrows, no net nitrification was detected, despite high NH þ 4 availability and frequent O 2 injections by larval ventilation activity. Conversely, burrows were sites of NH þ 4 production and NO 2 3 consumption. Nevertheless, the abundance of nitrifying bacteria increased measurably in the burrowing layer after prolonged incubation, but only in sediments in which the larvae were able to construct and ventilate stable burrows.