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Abstract: Following basin-wide contamination from industrial emissions and urban development, total dissolved copper concentrations in some regions of San Francisco Bay have exceeded national and state guidelines for water quality. In the face of dramatic improvements in wastewater treatment and point source control, persisting elevated dissolved copper concentrations in the Bay have prompted multiple studies and extensive monitoring of this estuary since 1989. Statistical analyses of monitoring data show that total dissolved copper concentrations have declined in the North (by 17%) and South (29%) San Francisco Bay as well as in the Southern Sloughs (44%) from 1993 to 2001. Concentrations remain elevated in the farthest reaches of the Bay (Delta and Estuary Interface), and in the Central Bay. Dissolved copper concentrations throughout the Bay have also been positively correlated (, , ) with dissolved organic matter, supporting results from complimentary chemical speciation studies which indicate that high-affinity copper-binding organic ligands dominate the chemical speciation of dissolved copper in the Bay. These organic ligands typically bind>99.9% of the dissolved copper, effectively buffering the system against small changes in dissolved copper concentrations, and maintaining free Cu2+ concentrations well below the toxicity threshold of ambient aquatic microorganisms. In response to these findings, site-specific water quality criteria for dissolved copper concentrations are now being developed by the Regional Water Quality Board to provide a more appropriate standard for copper toxicity in the Bay—one based on its chemical speciation and bioavailability. [Copyright &y& Elsevier]