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Purpose: This research aims to study the ecological risk of metals to Zostera japonica and focuses on two typical sediment environments in the Yellow River estuary, namely, sediment erosion and deposition areas. Materials and methods: Two different sediment habitats of Z. japonica were selected in this research from southern and northern sites in the Yellow River estuary. The plant growth and nutrient and metal concentrations in the sediments and Z. japonica tissue were investigated in the growth period of Z. japonica from April to October 2019. The shoot height of Z. japonica was measured with a centimetre-scale measuring stick, and the dry shoot weight was obtained after drying at 70 °C for 24 h. The total carbon (TC) and total nitrogen (TN) concentrations in the Z. japonica tissue and sediment were determined with an elemental analyser (Vario Macro Cube, Elementar Company, Germany). The total phosphorus (TP), iron (Fe), manganese (Mn), copper (Cu), zinc (Zn), lead (Pb), chromium (Cr) and cadmium (Cd) contents in the digested solutions were measured by high-resolution inductively coupled plasma atomic emission spectrometry (HR-ICP-AES, Spectro Company, Germany). Results and discussion: The growth of Z. japonica was different at the two study sites, with a higher biomass at the southern site than that at the northern site due to higher sediment nutrient concentrations at the southern site. The Cu, Zn, Pb, Cr and Cd concentrations in the sediments at the southern site were 25.1 μg g−1, 74.2 μg g−1, 21.4 μg g−1, 65.4 μg g−1 and 0.32 μg g−1, respectively, which were higher than the levels at the northern site of 13 μg g−1, 47.6 μg g−1, 12.4 μg g−1, 46.4 μg g−1 and 0.17 μg g−1, respectively. However, among the metals, only Cd was bioconcentrated in the Z. japonica tissue, with bioconcentration factor (BCF) values of 5.59 and 10.85 at the southern and northern sites, respectively. Conclusions: The sediments at the southern site in the estuary are composed of clays enriched in nutrients, thus supporting more sustainable growth and higher biomass than the coarse-particle sediments at the northern site in the estuary. Moreover, the sediments at the southern site were also enriched in metals, resulting in high levels of metals in the Z. japonica tissue. Overall, the ecological risk was low except for Cd, which should be considered because of its potential impacts on this seagrass and its related food webs in the estuary ecosystem. [ABSTRACT FROM AUTHOR]