In tropical Southeast Asia several species of seagrasses can often be found growing together on reef flats. These top-reef meadows are characterized by high temporal and spatial dynamics. Research conducted in the Spermonde Archipelago, Southwest Sulawesi, Indonesia, revealed that water motion and water depth are important structuring agents which influence the species composition of mixed meadows. Furthermore, burrowing alpheid and callianassid shrimp fulfill important roles in the meadows by enhancing nutrient recycling and controlling the lower boundary of the meadows. It is concluded that both abiotic (water motion and depth) and biotic (e.g. shrimp activity) factors affect the capacity of top-reef seagrass meadows to process and sequester carbon. The potential impact of sea level rise on these meadows, their influence on the sediment supply of nearby reef islands, and the advantages and disadvantages of different unmanned aerial monitoring systems such as kites, balloons and drones are discussed.