Coastal vegetated ecosystems, such as salt marshes, seagrass meadows, and mangrove forests, are valued for the ecosystem services they provide, including coastal protection, fisheries enhancement, and carbon sequestration. However, these systems have been declining globally, due to both natural and anthropogenic causes such as land conversion, pollution, eutrophication, and climate change impacts. Coastal management through ecosystem restoration and conservation aims to preserve or enhance these important habitats and is regulated and incentivized by international treaties like the Convention on Biological Diversity and the Paris Climate Agreement. Nevertheless, the management of coastal vegetated ecosystems and their services has to be informed by knowledge of the processes governing their provision across space and time and methods for their observation and evaluation have to be developed. This dissertation aims to fill recently identified knowledge gaps by providing estimates of carbon sequestration of seagrass meadows and salt marshes in an arid Eastern Pacific estuary. Here, seagrasses do not accumulate meaningful sedimentary carbon stocks but contribute exported organic matter to carbon buried in adjacent salt marsh sediments. Overall high proportions of allochthonous organic matter in salt marsh and benthic sediments suggest that current carbon accounting methodologies restricted to autochthonous carbon are not well suited to capture the carbon burial potential in systems with high organic matter fluxes between habitats. Leveraging recent advances in sensor technologies, this work shows how unmanned aerial vehicles and novel satellite platforms can allow mapping of seagrass meadows in a bay with turbid waters, from the meadow to ecosystem scale. Lastly, effects of disturbance on microbially-mediated nutrient cycling in mangrove-associated sediments of an urban tropical estuary are investigated using a metabarcoding approach. This dissertation centers on elemental cycling in sediments of mangroves, seagrasses, and salt marshes of previously understudied systems, namely an arid lagoon and a tropical urban estuary, with methods spanning scales from DNA sequencing to satellite remote sensing.
