Seagrass beds are valuable coastal ecosystems and are also of economic importance. For the first time, we measured the levels of heavy metals (copper, lead, cadmium, and zinc) in the environment and in the bodies of benthic biota within a seagrass bed in Liusha Bay, Guangdong Province. The results revealed that concentrations of heavy metals in the water column and sediment were relatively low and of little potential threat to the ecosystem. The average concentrations of copper, lead, and zinc in the water column were (2.2±0.1) μg/L, (0.8±0.2) μg/L, and (7.0±0.3) μg/L, respectively. Cadmium was not detected in the water column. The average concentrations of copper, lead, cadmium, and zinc in the surface of the sediment were (8.2±0.3) μg/L, (17.3±1.2) μg/L, (0.10±0.2) μg/L, and (11.9±0.2) μg/L, respectively. The ratios of metal concentration in water compared with sediment were 3 791, 21 625, 2 900, and 1681 for copper, lead, cadmium, and zinc, respectively. In contrast the levels of metals, especially cadmium, were markedly high in the bodies of macro-benthos such as the green algae, seagrasses, mollusca, and gastropods. The average concentrations of copper, lead, cadmium, and zinc in the green algae were 320, 21.0, 0.59 μg/L, and 142 μg/L, respectively. The average concentrations of copper, lead, cadmium, and zinc in the seagrasses were 13.2, 10.6, 1.00 μg/L, and 72.2 μg/L, respectively. The average concentrations of copper, lead, cadmium, and zinc in the bodies of mollusca were 1.9, 0.6, 1.0 μg/L, and 13.3 μg/L, respectively. The average concentrations of copper, lead, cadmium, and zinc in the bodies of gastropods were 5.3, 1.5, 0.15 μg/L, and 21.4 μg/L, respectively. The biological concentrating factors of benthic flora were generally greater than those of benthic fauna. The average biological concentrating factors for copper, lead, cadmium, and zinc in the green algae were 145.45, 26.25, 11.80, and 20.29, respectively. The average biological concentrating factors for copper, lead, cadmium, and zinc in the seagrasses were 6.00, 13.25, 20.00, and 10.31, respectively. The average biological concentrating factors for copper, lead, cadmium, and zinc in the bodies of mollusca were 0.86, 0.75, 20.00, and 1.90, respectively. The average biological concentrating factors for copper, lead, cadmium, and zinc in the bodies of gastropods were 2.41, 1.88, 3.00, and 3.06, respectively. The maximum biological concentrating factor was found for copper, in the alga Cladophora glomerata. Higher levels of copper, lead, and zinc were found in the green algae than in the seagrass. Lower levels of copper, lead, and zinc were concentrated in the bodies of mollusca than in the gastropods. For cadmium, the patterns of enrichment were reversed. This indicated that the dynamics of enrichment for cadmium might be very different from those of copper, lead, and zinc. Meanwhile, of these four metals, the biological concentrating factor of cadmium was the highest in seagrasses and mollusca. It was also the second highest in gastropods. In contrast, the biological concentrating factor of cadmium was the lowest of the four metals in the green algae. This indicated that the dynamics of enrichment for cadmium in the green algae might be very different from those in seagrasses, mollusca, and gastropods. The concentrations of lead and cadmium in the bodies of mollusca greatly exceeded the first levels of Marine Biological Quality (GB18421-2001, lead: 0.1mg/kg; cadmium: 0.2mg/kg). The greatest quality index (16.2) was found for cadmium in the bodies of Barbatia fusca, indicating that there was cadmium discharging near the seagrass meadow.