The sediments of mangrove forests and seagrass beds are significant sinks for atmospheric carbon dioxide. If researchers can show that constructed mangrove forests and seagrass beds accumulate and store carbon, carbon storage may become a strong incentive to build and restore these ecologically-important systems. This study compares sediment organic carbon pools (total, labile, and microbial biomass) and organic carbon sources in a recently built mangrove and seagrass system and in adjacent reference systems in the Indian River Lagoon, Florida. Pools and sources were measured at depths of 0-5 cm and 5-10 cm in the sediments and in the algal, litter, or floc layer on top of the sediments. Sampling occurred at the middle and end of the growing season. Major sources to sediment organic carbon were determined using ¹³C and ¹⁵N stable isotopes. The constructed seagrass system had larger organic carbon pools than the constructed mangrove system, which was probably due to the subaqueous condition of the seagrass sediments. While total sediment organic carbon of the constructed systems were much lower than in the reference systems, the magnitude of microbial biomass carbon concentrations were similar. Organic carbon in the constructed systems was more algal-derived than organic carbon in the reference systems. As the constructed systems are only a year old, it is too early to say whether they are effective carbon sinks. Currently they are storing carbon, but the carbon is coming from labile sources, is in pools with high turnover rates, and therefore is not likely stored long term.