Productivity measurements from carbon uptake have been suggested as good indicators of the physiological health of seagrasses. As seagrasses acquire carbon from the surrounding water, the rate of uptake often provide a good measure of the efficiency at which seagrasses meet their resource demands for growth. This rate is often used to assess the photosynthetic efficiency of the plants, a proxy for the physiological status of seagrass. This has special relevance to the Adelaide region as over 5000 ha of seagrasses have been lost from Adelaide coastal waters over the last 70 years, with much of this loss attributed to nutrient inputs from wastewater, industrial and stormwater discharges. This study used an in-situ inorganic carbon isotope-labelling and spike approach to obtain ecologically relevant estimates of seasonal variability in carbon uptake and its allocation in two species of temperate seagrass common to this coast (Amphibolis antarctica and Posidonia angustifolia). Uptake of carbon by the seagrass complex (leaves, roots, phytoplankton and epiphytes) was affected by both season and species. Carbon uptake rates of phytoplankton were generally higher than other components of the system. Uptake rates ranged from 0.01 mg C g−1 DW h−1 (summer) to 0.61 mg C g−1 DW h−1 (spring) in Posidonia and 0.02 mg C g−1 DW h−1 (summer) to 0.93 mg C g−1 DW h−1 (winter) in Amphibolis. Carbon uptake by the Amphibolis complex was higher than in the Posidonia complex. The Amphibolis complex had higher uptake rates in summer whereas the Posidonia complex was higher in spring. Fine sediments probably from a nearby dredging operation, are likely to have resulted in lower carbon uptake and a reduction in the above-ground and below-ground biomass in summer.