ABSTRACTThree species of bivalve mollusc Crassostrea gigas (Thunberg), Ostrea edulis L., Tapes philippinarum (Adams and Reeve), one species of crustacean, Homarus americanus, and one species of macroscopic algae Gracilariopsis sjostedtii were grown in a pilot‐scale marine waste recycling aquaculture system for a period of 18 months. Organisms were exposed to 14 different regimes of food chain enrichment using either secondary treated sewage effluent, a mixture of inorganic nitrogen and phosphorus compounds free of contaminants, or a combination of both to simulate “growth” and “depuration” periods in an on‐site application. Throughout the study organisms were sacrificed at monthly intervals and assayed for 7 trace metals (Cd, Cr, Cu, Hg, Ni, Pb, Zn). Sewage effluent used for food chain enrichment was assayed for the same suite of metals three times per week. No significant differences were evident between organisms cultured in the contaminant‐free and effluent enriched regimes. Shellfish trace metal contents were consistently below FDA “alert” levels. H. americanus trace metal levels were within acceptable standards for human consumption. Trace metal levels in G. sjostedtii were comparable with those recorded for natural populations of macrophytes. Data suggest that trace metals constitute a minimal public health problem in organisms cultured for human consumption in waste recycling systems; however, problems related to organic residues and viruses have yet to be fully evaluated.