Nitrification rates were measured using intact sediment cores from South San Francisco Bay and two different nitrification inhibitors: acetylene and methyl fluoride. Sediment oxygen consumption and ammonium and nitrate fluxes were also measured in these cores. Four experiments were conducted in the spring, and one in the fall of 1993. There was no significant difference in nitrification rates measured using the two inhibitors, which suggests that methyl fluoride can be used as an effective inhibitor of nitrification. Nitrification was positively correlated with sediment oxygen consumption and numbers of macrofauna. This suggests that bioturbation by macrofauna is an important control of nitrification rates. Irrigation by the tube-dwelling polychaete, Asychis elongata, which dominates the benthic biomass at this location, appears particularly important. Ammonium fluxes out of the sediment were greatest about one week after the spring bloom, while nitrification peaked about one month later.