Sediment in the vicinity of Hunters Point in San Francisco Bay, particularly from the region of the U.S. Naval Shipyard and nearby power plant, are considered to be among the most polluted in the bay, especially with regard to the metals arsenic, chromium, cadmium, copper, lead, nickel, zinc, and mercury, as well as numerous organic compounds. Benthic foraminifera recovered from this location in 1986 and 1997 exhibit distinct reddish-brown encrustations on their tests. Energy Dispersive X-ray analysis (EDAX), Energy dispersive X-ray spectroscopy (EDS), and electron microprobe analysis (EMA) of these encrustations determined that they are composed of iron, phosphorus, aluminum, magnesium, sodium, manganese, and sulfur. The Asian foraminifera Trochammina hadai, introduced into San Francisco Bay in the early 1980s, is most commonly affected, although Ammonia kitazatoi are also rarely impacted. Sixty-six to 78% of the T. hadai specimens, comprising over one-third to more than one-half of the foraminiferal assemblage collected in September 1986, shows evidence of these encrustations, whereas only 3% of those recovered in July 1997 were affected. Fourteen black-encrusted specimens of T. hadai, comprising 4% of the assemblage, and two affected ostracod carapaces were also found in one sample collected in the subembayment of Richardson Bay in August 1997. At both locations, the encrustations most often occur on the dorsal side of the foraminiferal tests, although in severe cases, both dorsal and ventral sides are involved with nearly all of the test chambers obscured. Evidence suggests that the encrustations occur at or near the sediment-water interface and do not appear to be a post-mortem effect. The presence of desiccated extracellular polymeric substances on some specimens is a good indicator of biofilms, suggesting the encrustations are microbially-facilitated. The seasonal variability in abundance of encrustations does not appear to be due to changes in temperature or salinity, but instead may reflect cessation of reproduction during the summer versus autumn sampling months.