The downward transition from aerobic to anaerobic conditions in a harbor mud is not simply a function of the biological consumption of oxygen. It is also controlled by the amount of soluble iron (Fe2+) and microbially‐generated hydrogen sulfide available to coprecipitate as acid‐soluble sulfide (FeS). In this way both the chemistry and the microbiology of these sediments govern the iron and sulfur speciation as well as the depth of the aerobic zone.