Together with Coral reefs and mangrove forests, seagrass meadows rank amongst the most important ecosystem components of tropical coastlines. The highly productive seagrasses support large biomasses of fishes and invertebrates, and are the preferred food item of iconic endangered species like green turtles and dugongs. Southeast Asia has the greatest diversity of seagrasses worldwide, and a substantial part of the global seagrass area. In spite of that, seagrasses in the region remain poorly studied. Research conducted in the Spermonde archipelago by scientists of the AWI in collaboration with representatives of Hasanuddin University Makassar aimed to fill some of the knowledge gaps on Southeast Asian seagrass ecosystems. In the first phase of the project the impact of seaweed farming on the productivity of the seagrass meadow below was adressed. The second focus was on the ecological role of synaptid holothurians, burrowing axiid shrimp and siganid fishes in the meadows. The biodiversity of gobiid fishes and plankton was also studied. In the second phase the main focus was on seagrass distribution, the impact of water motion and water depth on the composition of multispecies meadows, the controlling effect of callianassid shrimp and the diversity and diet of fish communities. Pinnid bivalves, macrobenthos diversity and plankton processes were the subject of further studies. In the third phase an in-situ carbon dioxide enrichment experiment was conducted, and the magnitude and fate of river inputs into the Spermonde lagoon was measured. In all three phases, capacity building was done through jointly supervised final theses and lectures in the “Marine Ecology Special Training Course”. Seventeen German and ten Indonesian students wrote their thesis within the project. A total of four PhD, 15 master and eight bachelor theses were completed.