Seagrasses increase sediment complexity by trapping particulates and influencing biogeochemical cycles via root oxygen loss and organic matter exudation. However, their impact on trace metal sequestration is poorly studied. We found significantly higher trace metal concentrations in seagrass sediments compared to adjacent bare sediments, correlating with total organic carbon, iron, and fine sediments. Sequential extractions showed that most trace metals were dominated by recalcitrant fractions (oxidizable and residual fractions), representing phases such as organic matter, iron sulfides, and crystalline iron oxides. Depth-dependent trends in trace metal partitioning were evident. For example, arsenic in the oxidizable fraction only weakly correlated with Fe in surface sediments (r sp = 0.55) but correlated strongly in deeper sediments (r sp = 0.87), consistent with iron sulfides being a dominant host-phase. Overall, these results suggest that the unique geochemical conditions facilitated by seagrasses play an important role in sequestering trace metals in urban estuarine sediments.