The 1994 spring phytoplankton bloom in South San Francisco Bay caused substantial reductions in concentrations of dissolved Cd, Ni, and Zn, but not Cu. We estimate that the equivalent of ~60% of the total annual input of Cd, Ni, and Zn from local waste‐water treatment plants is cycled through the phytoplankton in South Bay. The results suggest that processes that affect phytoplankton bloom frequency or intensity in estuaries (e.g. nutrient enrichment) may also affect metal trapping. The bloom was characterized by hydrographic surveys conducted at weekly intervals for 9 weeks. Metal samples were collected from the water column on three occasions, timed to bracket the period when the bloom was predicted. Factors that might confound observations of biological influences, such as freshwater inputs, were relatively constant during the study. Before the bloom, concentrations of dissolved Cd were 0.81 ± 0.02 nmol kg⁻¹, Zn concentrations were 19.8 ± 1.5 nmol kg⁻¹, Ni were 42 ± 1.4 nmol kg⁻¹, and Cu were 37 ± 1.4 nmol kg⁻¹. These values are elevated relative to riverine and coastal end‐members, reflecting inputs from wastewater and(or) sediments. At the height of the bloom, dissolved Zn, Cd, and Ni were reduced to 19, 50, and 75% of their prebloom concentrations, respectively. Dissolved Cu concentrations increased 20%. The mass of Cd taken up by phytoplankton was similar to the mass of Cd removed from solution if particle settling was considered, and Cd concentrations estimated in phytoplankton were higher than concentrations in suspended particulate material (SPM). Particulate concentrations of Zn and Ni during the bloom appeared to be dominated by the influence of changes in resuspension of Zn and Ni‐rich sediments.