The sediment trap experiments have been carried out during the 2001/2002 El Ni¿o/La Ni¿a transition in the monsoon-driven and freshwater influenced upwelling system off South Java. The results indicate that enhanced precipitation rates and associated river discharges increase the CO2-uptake of the biological pump by increasing the organic carbon export and reducing the carbonate precipitation. The freshwater, furthermore, forms a buoyant low salinity surface layer that caps off the nutrient and CO2-rich subsurface waters which shortens the upwelling season during wet La Ni¿a conditions. A reduced capping-effect during dryer El Ni¿o conditions strengthens the upwelling and as shown by our model results increase CO2 emission into the atmosphere along the freshwater influenced continental margins in SE Asia. By contrast El Ni¿o weakens upwelling and reduces the CO2 emission in the equatorial Pacific Ocean.