Analyses of the benthic community structure of a mudflat in South San Francisco Bay over a 29-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinal clam Macoma balthica from the same area. The community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that could be indicative of a more stable community that is subjected to less stress. In addition, two of the opportunistic species (Ampelisca abdita and Streblospio benedicti) that brood their young and live on the surface of the sediment in tubes have shown a continual decline in dominance coincident with the decline in metals. Heteromastus filiformis, a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying their eggs on or in the sediment has shown a concurrent increase in dominance. These changes in species dominance reflect a change in the community from one dominated by surface dwelling, brooding species to one with species with varying life history characteristics. Analysis of the reproductive activity of Macoma balthica shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissue of this organism. Reproductive activity is presently stable with almost all animals reproducing during the two reproductive seasons (spring and fall) of most years. These findings are consistent with findings previously reported for the 1974 through 2002 period.