Seagrass meadows are effective carbon sinks, sequestering atmospheric CO₂ and capturing allochthonous organic material, storing organic carbon (C_org) in their sediments, so called Blue Carbon. In tropical areas, seagrass meadows have a high number of calcareous organisms, which can offset carbon sequestration by releasing CO₂ through their calcification. Human activities such as urbanization and land-use change with inadequate management of blue carbon ecosystems are causing fast degradation of tropical blue carbon ecosystems, particularly mangroves and seagrasses. In this thesis, I and colleagues looked at the carbon sequestration process and the impact of marine protected areas (MPAs) on C_org conservation in the blue carbon ecosystems of the western Indian Ocean (WIO) region. This was accomplished by examining the air-water CO₂ flux in different plant community compositions (i.e. seagrass and calcifying macroalgae), as well as factors driving air-water CO₂ flux and the assessment of C_org stocks within and outside MPAs in tropical and subtropical areas of the WIO. The impact of landscape configuration and modification due to urbanization and mangrove degradation on the accumulation and variability of C_org in seagrass habitats was also investigated. We found that, the sum of the fluxes showed a net efflux of CO₂ over the meadows. The CO₂ fluxes changed both in rate and direction over the day, and were significantly related to plant community composition and environmental conditions  such as pH and CO₂ partial pressure, where pH had the strongest influence on CO₂ fluxes. Influxes were found only over vegetation with high proportion of seagrass and in the afternoon, whereas calcifying algae appeared to reverse the flow. We found that highly productive seagrass meadows can generate a net CO₂ from the water to the atmosphere as plants’ demand for CO₂ to a large extent is covered by internal cycling of CO₂, both from degradation of autochthonous and allochthonous material and calcification. We found that accumulation of C_org in seagrass meadows is larger than the flow to the atmosphere, indicating that these systems can still be carbon sinks.

The inflow of allochthonous carbon, C_org content and stocks in the seagrass meadows was influenced by a combination of landscape metrics and inherent habitat plant- and sediment-properties. We discovered a strong land to sea gradient in terms of C_org content in seagrass seascapes, due to hydrodynamic forces that resulted into unique patterns in sedimentary C_org levels. Seagrass surface sediments closer to a deforested mangrove had higher C_org content and mangrove signal, probably due to increased C_org export from deforested mangrove. In comparison to more diversified and patchy seascapes, seascapes with extensive continuous seagrass meadows have higher sedimentary C_org content. Seagrass meadows located near an area with rapid and short-term urbanization and degraded mangroves had a higher sedimentary C_org content, but similar carbon accumulation rate as an area with long-term progressive urbanization. It was found that tropical and subtropical blue carbon ecosystems store a significant amount of carbon in their sediments, but that many carbon storage hotspots are entirely/partially outside MPAs. This masks their influence on blue carbon conservation. MPAs can still be used to conserve blue carbon if carbon hotspots are properly located and managed.

This thesis contributes knowledge of important determining factors influencing primary pathways of tropical coastal ecosystem carbon sequestration and are critical for identifying hotspots of carbon storage to generate conservation prioritizations.  Future research should focus on conservation prioritizations that will limit the unsustainable use of coastal resources.