Salt marsh sediment serves an important ecological service by sequestering carbon but is also a repository for several pollutants including heavy metals. Metal uptake in marshes is affected by numerous environmental characteristics such as sediment pH and redox potential, but anthropogenic activities have also been adding metal loads to these fragile ecosystems. This metal deposition can have negative effects both environmentally and on human health. This study aims to better characterise the concentrations of six metals (arsenic (As), copper (Cu), manganese (Mn), zinc (Zn), lead (Pb), nickel (Ni)) in the sediment of two salt marshes in Massachusetts (United States of America). Metal loadings were compared (1) between anthropogenic loadings (i.e., a rural versus urban site); (2) seasonally; and (3) across native and invasive vegetation types. Heavy metal concentrations were analysed using a Handheld XRF instrument. There was a significant difference (p-value < 0.05) between the urban samples and rural samples, with the urban marsh showing higher rates of metal pollution. There was no significant difference (p-value > 0.05) seasonally among these metals but sediment samples under the invasive plant vegetation (Phragmites australis) had significantly higher (p-value < 0.05) metal concentrations compared to those samples under native plant vegetation (Spartina alterniflora). This study serves as a foundation for making future predictions in the face of climate change as more people move to urban areas, average atmospheric temperatures increase and precipitation patterns change, and sea level rise changes plant zonation.