San Diego Bay is heavily contaminated with metals, but little is known about their biological availability to local marine organisms. This study on 15 elements showed that concentrations of metals associated with sediment increased from the mouth to the back of the Bay while metals in seawater particulates were similar throughout the Bay. Metal bioavailability was assessed over 8 weeks following transplant of the local brittlestar, Ophiothrix spiculata (Ophuroidea, Echinodermata), from outside to inside the Bay. Despite a gradient of contamination, brittlestars accumulated similar levels of metals throughout the Bay, suggesting that metal contamination occurred through dissolved metals as well as through the diet. Sediment transplanted in dialysis tubing in the Bay accumulated metals only when placed on the seafloor bottom, indicating greater metal bioavailability near the bottom; the level of accumulation was similar between the mouth and the back of the Bay. The results are consistent with a circulation pattern in which a bottom layer of seawater, enriched with metals, drains from the back to the mouth of the Bay. There was a positive correlation between metal concentration in brittlestars and tidal range, suggesting increased metal exposure due to bay-ocean water exchange. For brittlestar arms the correlation was higher at the mouth than the back of the Bay, indicating greater metal accumulation in arms from dissolved metals in seawater than from ingestion of metal contaminated diet. In contrast, for brittlestar disks the correlation was higher at the back of the Bay, indicative of metal accumulation mainly through the diet. The results highlight the importance of considering bioavailability and physical processes in environmental quality assessments.