Coastal blue carbon habitats perform many important environmental functions, including long-term carbon and anthropogenic contaminant storage. Here, we analysed twenty-five 210Pb-dated mangrove, saltmarsh, and seagrass sediment cores from six estuaries across a land-use gradient to determine metal, metalloid, and phosphorous sedimentary fluxes. Cadmium, arsenic, iron, and manganese had linear to exponential positive correlations between concentrations, sediment flux, geoaccumulation index, and catchment development. Increases in anthropogenic development (agricultural or urban land uses) from >30 % of the total catchment area enhanced mean concentrations of arsenic, copper, iron, manganese, and zinc between 1.5 and 4.3-fold. A ~ 30 % anthropogenic land-use was the threshold in which blue carbon sediment quality begins to be detrimentally impacted on an entire estuary scale. Fluxes of phosphorous, cadmium, lead, and aluminium responded similarly, increasing 1.2 to 2.5-fold when anthropogenic land-use increased by at least 5 %. Exponential increases in phosphorus flux to estuary sediments seem to precede eutrophication as observed in more developed estuaries. Overall, multiple lines of evidence revealed how catchment development drives blue carbon sediment quality across a regional scale.